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NCBI C++ ToolKit: GUI_PKG_ALIGNMENT

typedef vector< CConstRef< objects::CSeq_annot > >  CAnnotCompareView::TAnnotVector   typedef vector< CConstRef< objects::CSeq_align > >  CAnnotCompareView::TAlignVector   typedef map< wxString, CRef< CBLAST_Dlg_Item > >  CBLAST_Dlg_Item::TNameToItemMap   typedef CBLASTDatabases::TDbMap  CBLAST_DB_Dialog::TDbMap   typedef deque< CBLAST_Dlg_Item * >  CBLAST_DB_Dialog::TItemDeque   typedef vector< CRef< CNetBlastJobDescriptor > >  CNetBlastSubmittingJob::TDescriptors   typedef vector< CRef< CNetBlastJobDescriptor > >  CNetBlastMonitoringJob::TDescriptors   typedef vector< CRef< CNetBlastJobDescriptor > >  CNetBlastLoadingJob::TDescriptors   typedef CMRUList< string >  CBLASTParams::TMRUDatabases   typedef CMRUList< string >  CBLASTParams::TMRUQueries   typedef set< string, PNocase >  CBLASTParams::TRepeatLibs   typedef map< blast::EProgram, const SProgInfo * >  CBLASTParams::TProgramAttrMap   typedef map< blast::EProgram, SProgParams >  CBLASTParams::TProgramParamsMap   typedef vector< CRef< CNetBlastJobDescriptor > >  CBlastSearchTask::TDescriptors   typedef map< string, TConstScopedObjects >  CClustalOmegaTool::TObjects   typedef map< string, TConstScopedObjects >  CClustalwTool::TObjects   typedef CRef< objects::CLoaderDescriptor >  CCreateGeneModelTask::TLoaderRef   typedef CRef< objects::CProjectItem >  CCreateGeneModelTask::TItemRef   typedef list< SGeneCdsmRnaFeats >  CCreateGeneModelTask::TGeneCDSmRNAList   a loader might be tied with a specific project item. More...
  typedef map< objects::CSeq_id_Handle, TGeneCDSmRNAList >  CCreateGeneModelTask::TGeneModelMap   typedef vector< CConstRef< objects::CSeq_align > >  CDotMatrixView::TAlignVector   typedef map< string, TConstScopedObjects >  CKalignTool::TObjects   typedef map< string, TConstScopedObjects >  CMafftTool::TObjects   typedef vector< CIRef< IProjectView > >  CMPCrossAlignView::TViews   typedef pair< CConstRef< objects::CSeq_loc >, CRef< objects::CScope > >  CMSAToolJob::TLocPair   typedef map< string, TLocPair >  CMSAToolJob::TIdMap   typedef map< objects::CSeq_id_Handle, bool >  CMSAToolJob::TSeqTypeMap   typedef map< string, TConstScopedObjects >  CMuscleTool::TObjects   typedef set< CNetBlastJobDescriptor::EState >  CNetBLAST_DMSearchQuery::TStates   typedef pair< const char *, const char * >  CNetBLAST_DMSearchJob::TPair   typedef vector< CRef< CNetBlastJobDescriptor > >  CNetBLASTUIDataSource::TJobDescrVec   typedef map< int, string >  CNetBLASTUIDataSource::TTaxIdLabelMap   typedef list< CConstRef< objects::CUser_field > >  CNetBLASTUIDataSource::TUserFields   typedef map< string, TConstScopedObjects >  CProSplignTool::TObjects   typedef map< string, TConstScopedObjects >  CSplignTool::TObjects   typedef map< string, TConstScopedObjects >  CCommonTaxTreeTool::TObjects   enum   {
  CBLAST_DB_Dialog::ID_CBLAST_DB_DIALOG = 10012 , CBLAST_DB_Dialog::ID_SEARCH = 10015 , CBLAST_DB_Dialog::ID_RESET_BTN = 10016 , CBLAST_DB_Dialog::wxID_STATUS = 10017 ,
  CBLAST_DB_Dialog::ID_TREECTRL = 10014
}   enum   {
  CBLASTSearchOptionsPanel::ID_CBLASTSEARCHOPTIONSPANEL = 10000 , CBLASTSearchOptionsPanel::ID_NUC_RADIO = 10001 , CBLASTSearchOptionsPanel::ID_PROT_RADIO = 10002 , CBLASTSearchOptionsPanel::ID_QUERY_SEQ_SET = 10042 ,
  CBLASTSearchOptionsPanel::ID_LIST = 10003 , CBLASTSearchOptionsPanel::ID_PROGRAM_COMBO = 10004 , CBLASTSearchOptionsPanel::ID_RADIOBUTTON = 10040 , CBLASTSearchOptionsPanel::ID_RADIOBUTTON2 = 10010 ,
  CBLASTSearchOptionsPanel::ID_RADIOBUTTON1 = 10041 , CBLASTSearchOptionsPanel::ID_SUBJECT_SEQ_SET = 10043 , CBLASTSearchOptionsPanel::ID_SUBJ_LIST = 10012 , CBLASTSearchOptionsPanel::ID_DB_COMBO = 10005 ,
  CBLASTSearchOptionsPanel::ID_SELECT_NCBI_DB = 10006 , CBLASTSearchOptionsPanel::ID_ENTREZ_COMBO = 10007 , CBLASTSearchOptionsPanel::ID_TEXTCTRL = 10011 , CBLASTSearchOptionsPanel::ID_SELECT_LOCAL_DB_BTN = 10026 ,
  CBLASTSearchOptionsPanel::ID_CHECKBOX = 10039
}   enum   { CBLASTSearchOptionsPanel::ID_DBS_LOADING_TEXT = 10030 , CBLASTSearchOptionsPanel::ID_DBS_LOADING_PROGRESS = 10031 , CBLASTSearchOptionsPanel::ID_DBS_FAILED = 10032 , CBLASTSearchOptionsPanel::ID_DBS_TRY_AGAIN = 10033 }   enum   CBLASTParams::ESubjectType { CBLASTParams::eSequences , CBLASTParams::eNCBIDB , CBLASTParams::eLocalDB }   enum   {
  CBLASTSearchParamsPanel::ID_CBLASTSEARCHPARAMSPANEL = 10000 , CBLASTSearchParamsPanel::ID_WORDSIZE = 10019 , CBLASTSearchParamsPanel::ID_E_VALUE = 10020 , CBLASTSearchParamsPanel::ID_THRESHOLD = 10018 ,
  CBLASTSearchParamsPanel::ID_GEN_CODE = 10024 , CBLASTSearchParamsPanel::ID_COMBOBOX = 10003 , CBLASTSearchParamsPanel::ID_LOW_COMPLEXITY = 10021 , CBLASTSearchParamsPanel::ID_STATIC_REPEAT_TYPE = 10037 ,
  CBLASTSearchParamsPanel::ID_REPEAT_TYPE = 10032 , CBLASTSearchParamsPanel::ID_MASK_LOWERCASE = 10002 , CBLASTSearchParamsPanel::ID_MASK_REPEATS = 10001 , CBLASTSearchParamsPanel::ID_WMTI_CHOICE = 10035 ,
  CBLASTSearchParamsPanel::ID_BUTTON = 10036 , CBLASTSearchParamsPanel::ID_ADV_TEXT = 10008 , CBLASTSearchParamsPanel::ID_COMPARTMENTS = 10038 , CBLASTSearchParamsPanel::ID_TITLE_TEXT = 10009 ,
  CBLASTSearchParamsPanel::ID_STANDALONE = 10033
}   enum   { CBLASTSearchParamsPanel::ID_LOADING_TEXT = 10100 , CBLASTSearchParamsPanel::ID_LOADING_PROGRESS = 10101 }   enum   CBlastSearchTask::ECommand {
  CBlastSearchTask::eInvalid = -1 , CBlastSearchTask::eSubmit , CBlastSearchTask::eMonitor , CBlastSearchTask::eRetrieve ,
  CBlastSearchTask::eFinished
}   enum   CBLASTToolManager::EState { CBLASTToolManager::eInvalid = -1 , CBLASTToolManager::eOptions , CBLASTToolManager::eParams , CBLASTToolManager::eCompleted }   enum   SCleanupAlignmentsParams::EAlgorithm { SCleanupAlignmentsParams::eHitFilter , SCleanupAlignmentsParams::eAlignmentManager }   which algorithm are we using? More...
  enum   {
  CCleanupAlignmentsParamsPanel::ID_CCLEANUPALIGNMENTSPARAMSPANEL = 10013 , CCleanupAlignmentsParamsPanel::ID_LISTCTRL2 = 10014 , CCleanupAlignmentsParamsPanel::ID_COMBOBOX = 10015 , CCleanupAlignmentsParamsPanel::ID_TEXTCTRL1 = 10017 ,
  CCleanupAlignmentsParamsPanel::ID_TEXTCTRL = 10016 , CCleanupAlignmentsParamsPanel::ID_CHECKBOX1 = 10019 , CCleanupAlignmentsParamsPanel::ID_CHECKBOX2 = 10020 , CCleanupAlignmentsParamsPanel::ID_CHECKBOX = 10018 ,
  CCleanupAlignmentsParamsPanel::ID_CHECKBOX5 = 10033
}   enum   {
  CFindOverlapPanel::ID_CFINDOVERLAPPANEL = 10021 , CFindOverlapPanel::ID_LISTCTRL3 = 10022 , CFindOverlapPanel::ID_LISTCTRL4 = 10023 , CFindOverlapPanel::ID_TEXTCTRL2 = 10024 ,
  CFindOverlapPanel::ID_TEXTCTRL4 = 10026 , CFindOverlapPanel::ID_TEXTCTRL5 = 10027
}   enum   {
  CGroupAlignmentsParamsPanel::ID_CGROUPALIGNMENTSPARAMSPANEL = 10002 , CGroupAlignmentsParamsPanel::ID_LISTCTRL = 10004 , CGroupAlignmentsParamsPanel::ID_CHECKBOX_SEQID = 10005 , CGroupAlignmentsParamsPanel::ID_CHECKBOX_STRAND = 10006 ,
  CGroupAlignmentsParamsPanel::ID_CHECKBOX_TAXID = 10000 , CGroupAlignmentsParamsPanel::ID_CHECKBOX_SIMILAR_TAXID = 10001 , CGroupAlignmentsParamsPanel::ID_CHECKBOX_REFSEQ = 10007 , CGroupAlignmentsParamsPanel::ID_CHECKBOX_EST = 10008 ,
  CGroupAlignmentsParamsPanel::ID_CHECKBOX_REFSEQ_PREDICTED = 10009 , CGroupAlignmentsParamsPanel::ID_CHECKBOX_GENBANK = 10010 , CGroupAlignmentsParamsPanel::ID_CHECKBOX_WGS = 10011 , CGroupAlignmentsParamsPanel::ID_CHECKBOX_HTGS = 10012 ,
  CGroupAlignmentsParamsPanel::ID_CHECKBOX_PATENT = 10003
}   enum   {
  CMergeAlignmentsParamsPanel::ID_CBLASTSEARCHOPTIONSPANEL = 10000 , CMergeAlignmentsParamsPanel::ID_LISTCTRL1 = 10003 , CMergeAlignmentsParamsPanel::ID_CHECKBOX6 = 10071 , CMergeAlignmentsParamsPanel::ID_CHECKBOX7 = 10072 ,
  CMergeAlignmentsParamsPanel::ID_CHECKBOX8 = 10073 , CMergeAlignmentsParamsPanel::ID_CHECKBOX9 = 10074 , CMergeAlignmentsParamsPanel::ID_CHECKBOX10 = 10075
}   enum   CNeedlemanWunschToolParams::EFreeEndType { CNeedlemanWunschToolParams::eNone , CNeedlemanWunschToolParams::eLeft , CNeedlemanWunschToolParams::eRight , CNeedlemanWunschToolParams::eBoth }   enum   {
  CNetBlastDMSearchFormPanel::ID_CNETBLASTDMSEARCHFORM = 10023 , CNetBlastDMSearchFormPanel::ID_FILTER_INPUT = 10025 , CNetBlastDMSearchFormPanel::ID_SUBMITTED_CHECK = 10027 , CNetBlastDMSearchFormPanel::ID_COMPLETED_CHECK = 10028 ,
  CNetBlastDMSearchFormPanel::ID_FAILED_CHECK = 10029 , CNetBlastDMSearchFormPanel::ID_RETRIEVED_CHECK = 10030 , CNetBlastDMSearchFormPanel::ID_EXPIRED_CHECK = 10031
}   enum   CNetBlastJobDescriptor::EState {
  CNetBlastJobDescriptor::eInvalidState = -1 , CNetBlastJobDescriptor::eInitial , CNetBlastJobDescriptor::eSubmitted , CNetBlastJobDescriptor::eCompleted ,
  CNetBlastJobDescriptor::eFailed , CNetBlastJobDescriptor::eRetrieved , CNetBlastJobDescriptor::eExpired
}   enum   { CNetBLASTLoadOptionPanel::ID_NETBLASTLOADOPTIONPANEL = 10013 , CNetBLASTLoadOptionPanel::ID_TEXTCTRL1 = 10044 }   enum   ENetBlastCommands {
  eCmdRetriveBlastJobs = 12200 , eCmdMonitorBlastJobs , eCmdDeleteBlastJobs , eCmdExploreNetBLAST ,
  eCmdLoadRIDs , eCmdBlastWinMask
}   commands introduced by Net BLAST data source More...
  enum   CNetBLASTUIDataSourceEvent::EEventId { CNetBLASTUIDataSourceEvent::eJobDescrChanged }   enum   CNetBLASTUILoadManager::EState { CNetBLASTUILoadManager::eInvalid = -1 , CNetBLASTUILoadManager::eSelectRID , CNetBLASTUILoadManager::eSelectProject , CNetBLASTUILoadManager::eCompleted }   enum   { CPhyTreeView::kQueryPanelID = 6000 , CPhyTreeView::kPhylpWidgetID = 6001 }   enum   CMolTypeValidator::MolType { CMolTypeValidator::kGenomic , CMolTypeValidator::kCDNA , CMolTypeValidator::kProtein , CMolTypeValidator::kNucleotide }   enum   {
  CSplignPanel::ID_CSPLIGNPANEL = 10028 , CSplignPanel::ID_PANEL1 = 10029 , CSplignPanel::ID_PANEL2 = 10030 , CSplignPanel::ID_CHOICE3 = 10040 ,
  CSplignPanel::ID_CHOICE4 = 10076 , CSplignPanel::ID_CHECKBOX3 = 10034 , CSplignPanel::ID_CHECKBOX4 = 10035 , CSplignPanel::ID_TEXTCTRL7 = 10037 ,
  CSplignPanel::ID_TEXTCTRL6 = 10036 , CSplignPanel::ID_TEXTCTRL8 = 10038 , CSplignPanel::ID_TEXTCTRL9 = 10039 , CSplignPanel::ID_TEXTCTRL13 = 10043
}   enum   {
  CTreeBuilderPanel::ID_CTreeBuilderPanel = 10021 , CTreeBuilderPanel::ID_LISTCTRL3 = 10022 , CTreeBuilderPanel::ID_LISTCTRL4 = 10023 , CTreeBuilderPanel::ID_TEXTCTRL2 = 10024 ,
  CTreeBuilderPanel::ID_TEXTCTRL3 = 10025 , CTreeBuilderPanel::ID_TEXTCTRL4 = 10026 , CTreeBuilderPanel::ID_TEXTCTRL5 = 10027
}   enum   {
  CMuscleToolPanel::ID_CMUSCLEPANEL = 10050 , CMuscleToolPanel::ID_PANEL = 10051 , CMuscleToolPanel::ID_CHOICE2 = 10054 , CMuscleToolPanel::ID_CHECKBOX12 = 10053 ,
  CMuscleToolPanel::ID_TEXTCTRL11 = 10052 , CMuscleToolPanel::ID_TEXTCTRL12 = 10055 , CMuscleToolPanel::ID_BITMAPBUTTON1 = 10056
}   enum   { CNGAlignPanel::ID_CNGALIGNPANEL = 10047 , CNGAlignPanel::ID_QUERY_LIST = 10060 , CNGAlignPanel::ID_SUBJ_LIST = 10061 }   enum   CPslLoadManager::EState { CPslLoadManager::eInvalid = -1 , CPslLoadManager::eParams , CPslLoadManager::eCompleted }   enum   { CTaxTreeToolPanel::ID_CTAXTREETOOLPANEL = 10057 , CTaxTreeToolPanel::ID_PANEL3 = 10058 }   enum   CTextAlignLoaderManager::EState { CTextAlignLoaderManager::eInvalid = -1 , CTextAlignLoaderManager::eParams , CTextAlignLoaderManager::eCompleted }     CAlignSpanView::CAlignSpanView ()   void  CAlignSpanView::x_InitMenuResources ()   void  CAlignSpanView::x_InitWidget ()   virtual void  CAlignSpanView::x_UpdateStatusMessage ()   virtual void  CAlignSpanView::x_Update ()     CAnnotCompareView::CAnnotCompareView ()   virtual void  CAnnotCompareView::x_CreateMenuBarMenu ()   initializes m_MenuBarMenu; override in derived classes More...
  virtual const CObject *  CAnnotCompareView::x_GetOrigObject () const   void  CAnnotCompareView::x_InitWidget ()     CBLAST_Dlg_Item::CBLAST_Dlg_Item ()     CBLAST_Dlg_Item::CBLAST_Dlg_Item (const string &label, const string &path, bool is_database=false)     CBLAST_Dlg_Item::~CBLAST_Dlg_Item ()   wxString  CBLAST_Dlg_Item::GetLabel () const   const string &  CBLAST_Dlg_Item::GetPath () const   bool  CBLAST_Dlg_Item::IsDatabase () const   bool  CBLAST_Dlg_Item::IsVisible () const   void  CBLAST_Dlg_Item::SetVisible (bool visible)   bool  CBLAST_Dlg_Item::IsExpanded () const   void  CBLAST_Dlg_Item::Expand (bool expand)   CBLAST_Dlg_Item *  CBLAST_Dlg_Item::GetParent ()   TNameToItemMap *  CBLAST_Dlg_Item::GetChildItems ()   CBLAST_Dlg_Item *  CBLAST_Dlg_Item::GetChildByLabel (const string &label)   void  CBLAST_Dlg_Item::AddChild (CBLAST_Dlg_Item &item)   const wxTreeItemId &  CBLAST_Dlg_Item::GetId () const   void  CBLAST_Dlg_Item::SetId (const wxTreeItemId &id)     CBLAST_DB_Dialog::CBLAST_DB_Dialog ()     CBLAST_DB_Dialog::CBLAST_DB_Dialog (wxWindow *parent, wxWindowID id=ID_CBLAST_DB_DIALOG, const wxString &caption=wxEmptyString, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(400, 300), long style=wxCAPTION|wxRESIZE_BORDER|wxSYSTEM_MENU|wxCLOSE_BOX|wxTAB_TRAVERSAL)   bool  CBLAST_DB_Dialog::Create (wxWindow *parent, wxWindowID id=ID_CBLAST_DB_DIALOG, const wxString &caption=wxEmptyString, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(400, 300), long style=wxCAPTION|wxRESIZE_BORDER|wxSYSTEM_MENU|wxCLOSE_BOX|wxTAB_TRAVERSAL)     CBLAST_DB_Dialog::~CBLAST_DB_Dialog ()   void  CBLAST_DB_Dialog::Init ()   void  CBLAST_DB_Dialog::CreateControls ()   void  CBLAST_DB_Dialog::OnInitDialog (wxInitDialogEvent &event)   void  CBLAST_DB_Dialog::OnSearchTextUpdated (wxCommandEvent &event)   void  CBLAST_DB_Dialog::OnResetBtnClick (wxCommandEvent &event)   void  CBLAST_DB_Dialog::OnTreectrlSelChanged (wxTreeEvent &event)   void  CBLAST_DB_Dialog::OnTreectrlItemActivated (wxTreeEvent &event)   void  CBLAST_DB_Dialog::OnTreectrlItemCollapsed (wxTreeEvent &event)   void  CBLAST_DB_Dialog::OnTreectrlItemExpanded (wxTreeEvent &event)   void  CBLAST_DB_Dialog::OnOkClick (wxCommandEvent &event)   wxBitmap  CBLAST_DB_Dialog::GetBitmapResource (const wxString &name)   wxIcon  CBLAST_DB_Dialog::GetIconResource (const wxString &name)   static bool  CBLAST_DB_Dialog::ShowToolTips ()   void  CBLAST_DB_Dialog::SetToolName (const string &tool)   void  CBLAST_DB_Dialog::SetDBMap (const TDbMap &map)   void  CBLAST_DB_Dialog::SelectDatabases (vector< string > &databases)   void  CBLAST_DB_Dialog::GetSelectedDatabases (vector< string > &databases)   void  CBLAST_DB_Dialog::x_CreateItems ()   void  CBLAST_DB_Dialog::x_BuildTreeItems (CBLAST_Dlg_Item &item)   void  CBLAST_DB_Dialog::x_CreateTreeItems ()   void  CBLAST_DB_Dialog::x_FilterItems (const string &query)   void  CBLAST_DB_Dialog::x_UpdateCollapsedState (wxTreeItemId id)   void  CBLAST_DB_Dialog::x_UpdateFilterStatusText (bool reset, int n)   CBLAST_Dlg_Item *  CBLAST_DB_Dialog::x_GetSelectedDBItem ()   void  CBLAST_DB_Dialog::x_OnDatabaseSelected ()     CNetBlastSubmittingJob::CNetBlastSubmittingJob (string tool_name, const CBLASTParams &params, CNetBLASTUIDataSource &ds)   CNetBlastSubmittingJob. More...
  void  CNetBlastSubmittingJob::GetDescriptors (TDescriptors &descriptors)   void  CNetBlastSubmittingJob::GetErrors (vector< string > &errors) const   void  CNetBlastSubmittingJob::x_Run ()   this fucntions performs real work More...
  void  CNetBlastSubmittingJob::x_SetStatusText (const string &text)   void  CNetBlastSubmittingJob::x_ResetState ()   void  CNetBlastSubmittingJob::x_AddError (const string &error)     CNetBlastMonitoringJob::CNetBlastMonitoringJob (CNetBLASTUIDataSource &ds, IServiceLocator *srv_locator, const string &tool_name, TDescriptors &descriptors)   CNetBlastSubmittingJob. More...
  virtual void  CNetBlastMonitoringJob::SetLoadingOptions (CSelectProjectOptions &options)   EJobState  CNetBlastMonitoringJob::x_Run ()   this functions performs real work every call to this function does pools each job once, then functions exits if some of jobs are still pending it returns eRunning state, so that it can be executed one more time More...
  void  CNetBlastMonitoringJob::x_SetStatusText (const string &text)   void  CNetBlastMonitoringJob::x_ResetState ()   void  CNetBlastMonitoringJob::x_StartRetrivingTask (const vector< string > &RIDs)     CNetBlastLoadingJob::CNetBlastLoadingJob (CNetBLASTUIDataSource &ds, const vector< string > *RIDs=NULL, CScope *scope=NULL)   CNetBlastLoadingJob. More...
  void  CNetBlastLoadingJob::SetRIDs (CNetBLASTUIDataSource &ds, const vector< string > &RIDs)   bool  CNetBlastLoadingJob::HasErrors () const   void  CNetBlastLoadingJob::GetErrors (vector< string > &errors) const   virtual void  CNetBlastLoadingJob::x_CreateProjectItems ()   iterates on the given RIDs and creates Project Items or accumulates error More...
  void  CNetBlastLoadingJob::x_CreateProjectItemsFromBlastResult (objects::CSeq_align_set &results, CRef< blast::CRemoteBlast > RemoteBlast)     CBLASTSearchOptionsPanel::CBLASTSearchOptionsPanel ()     CBLASTSearchOptionsPanel::CBLASTSearchOptionsPanel (wxWindow *parent, wxWindowID id=ID_CBLASTSEARCHOPTIONSPANEL, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(), long style=wxTAB_TRAVERSAL)   bool  CBLASTSearchOptionsPanel::Create (wxWindow *parent, wxWindowID id=ID_CBLASTSEARCHOPTIONSPANEL, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(), long style=wxTAB_TRAVERSAL)     CBLASTSearchOptionsPanel::~CBLASTSearchOptionsPanel ()   void  CBLASTSearchOptionsPanel::Init ()   void  CBLASTSearchOptionsPanel::CreateControls ()   bool  CBLASTSearchOptionsPanel::TransferDataToWindow ()   bool  CBLASTSearchOptionsPanel::TransferDataFromWindow ()   void  CBLASTSearchOptionsPanel::OnNucRadioSelected (wxCommandEvent &event)   void  CBLASTSearchOptionsPanel::OnProtRadioSelected (wxCommandEvent &event)   void  CBLASTSearchOptionsPanel::OnQuerySequenceSetSelected (wxCommandEvent &event)   void  CBLASTSearchOptionsPanel::OnProgramComboSelected (wxCommandEvent &event)   void  CBLASTSearchOptionsPanel::OnSubjectSequencesSelected (wxCommandEvent &event)   void  CBLASTSearchOptionsPanel::OnSubjectNCBIDBSelected (wxCommandEvent &event)   void  CBLASTSearchOptionsPanel::OnSubjectLocalDBSelected (wxCommandEvent &event)   void  CBLASTSearchOptionsPanel::OnSubjectSequenceSetSelected (wxCommandEvent &event)   void  CBLASTSearchOptionsPanel::OnDatabaseComboSelected (wxCommandEvent &event)   void  CBLASTSearchOptionsPanel::OnBrowseDatabases (wxCommandEvent &event)   void  CBLASTSearchOptionsPanel::OnSelectLocalDB (wxCommandEvent &event)   void  CBLASTSearchOptionsPanel::OnLocalDBLoaderClick (wxCommandEvent &event)   wxBitmap  CBLASTSearchOptionsPanel::GetBitmapResource (const wxString &name)   wxIcon  CBLASTSearchOptionsPanel::GetIconResource (const wxString &name)   static bool  CBLASTSearchOptionsPanel::ShowToolTips ()   void  CBLASTSearchOptionsPanel::Setup (CNetBLASTUIDataSource &ds, const string &tool_name)   void  CBLASTSearchOptionsPanel::SetParams (CBLASTParams *params, map< string, TConstScopedObjects > *nuc_objects, map< string, TConstScopedObjects > *prot_objects)   void  CBLASTSearchOptionsPanel::SelectInputType ()   bool  CBLASTSearchOptionsPanel::CanDoNext ()   void  CBLASTSearchOptionsPanel::x_OnInputTypeChanged (bool nuc_input)   void  CBLASTSearchOptionsPanel::x_OnSubjInputTypeChanged ()   void  CBLASTSearchOptionsPanel::x_UpdateDBCombo ()   void  CBLASTSearchOptionsPanel::x_CheckDBLoaded ()   void  CBLASTSearchOptionsPanel::x_UpdateSubjects ()   void  CBLASTSearchOptionsPanel::OnTryAgain (wxCommandEvent &event)   void  CBLASTSearchOptionsPanel::OnTimer (wxTimerEvent &event)   void  CBLASTSearchOptionsPanel::x_UpdateSubjectType ()   void  CBLASTSearchOptionsPanel::x_UpdateQuerySeqSet ()   void  CBLASTSearchOptionsPanel::x_FillQueryList ()   void  CBLASTSearchOptionsPanel::x_UpdateSubjectSeqSet ()   void  CBLASTSearchOptionsPanel::x_FillSubjectList ()     CBLASTParams::SProgParams::SProgParams ()     CBLASTParams::SProgParams::SProgParams (int thresh, int word, double ev, bool low_c, int query_gen_code, int db_gen_code)     CBLASTParams::CBLASTParams ()   bool &  CBLASTParams::IsNucInput ()   bool  CBLASTParams::IsNucInput () const   TConstScopedObjects &  CBLASTParams::GetSeqLocs ()   const TConstScopedObjects &  CBLASTParams::GetSeqLocs () const   blast::EProgram &  CBLASTParams::GetCurrProgram ()   returns the current program for the currently selected input type More...
  const blast::EProgram  CBLASTParams::GetCurrProgram () const   blast::EProgram &  CBLASTParams::GetProgram (bool nuc)   returns the selected programs for the given input type More...
  const blast::EProgram  CBLASTParams::GetProgram (bool nuc) const   string &  CBLASTParams::GetCurrDatabase ()   returns the current database for the current program More...
  const string &  CBLASTParams::GetCurrDatabase () const   string &  CBLASTParams::GetDatabase (bool nuc_db)   returns the database of the specified type More...
  const string &  CBLASTParams::GetDatabase (bool nuc_db) const   TMRUDatabases &  CBLASTParams::GetCurrMRUDatabases ()   returns MRU databases for the current program More...
  TMRUDatabases &  CBLASTParams::GetMRUDatabases (bool nuc_db)   string &  CBLASTParams::GetEntrezQuery ()   string  CBLASTParams::GetEntrezQuery () const   bool  CBLASTParams::IsSubjNucInput () const   TConstScopedObjects &  CBLASTParams::GetSubjSeqLocs ()   const TConstScopedObjects &  CBLASTParams::GetSubjSeqLocs () const   SProgParams &  CBLASTParams::GetCurrParams ()   returns params for the current program More...
  const SProgParams &  CBLASTParams::GetCurrParams () const   void  CBLASTParams::ResetCurrParams ()   string &  CBLASTParams::GetAdvancedParams ()   string  CBLASTParams::GetAdvancedParams () const   static TRepeatLibs  CBLASTParams::GetAllRepeatLibs ()   static string  CBLASTParams::GetRepeatLib (const string &repeat_db)   static string  CBLASTParams::GetRepeatDb (const string &repeat_lib)   string &  CBLASTParams::GetJobTitle ()   string  CBLASTParams::GetJobTitle () const   bool  CBLASTParams::IsStandaloneRequested () const   void  CBLASTParams::StandaloneRequested (bool req)   bool  CBLASTParams::IsCompartmentsRequested () const   void  CBLASTParams::FindCompartments (bool req)   void  CBLASTParams::SetWM_Dir (const string &wm_dir_path)   const string &  CBLASTParams::GetWmDir () const   vector< string > &  CBLASTParams::ToArgVec (vector< string > &arg_vec) const   CArgs *  CBLASTParams::ToArgs (vector< string > &argv) const   CRef< blast::CBlastOptionsHandle >  CBLASTParams::ToBlastOptions (bool local=false) const   CRef< blast::CBlastOptionsHandle >  CBLASTParams::ToArgVecBlastOptions (vector< string > &arg_vec, bool local=true) const   objects::CUser_object *  CBLASTParams::ToUserObject () const   void  CBLASTParams::FromUserObject (const objects::CUser_object &user_obj)   static void  CBLASTParams::GetProgramLabels (bool nuc_input, vector< string > &labels)   static string  CBLASTParams::GetProgramLabel (blast::EProgram program)   static blast::EProgram  CBLASTParams::GetProgramByLabel (const string &str)   static bool  CBLASTParams::IsNucInput (blast::EProgram program)   static bool  CBLASTParams::IsNucDatabase (blast::EProgram program)   static bool  CBLASTParams::UseDustFilter (blast::EProgram program)   static bool  CBLASTParams::NeedsThreshold (blast::EProgram program)   static bool  CBLASTParams::NeedsDbGeneticCode (blast::EProgram program)   static bool  CBLASTParams::NeedsQueryGeneticCode (blast::EProgram program)   static int  CBLASTParams::GetGeneticCodeByLabel (const string &label)   static string  CBLASTParams::GetGeneticCodeLabel (int code_id)   static void  CBLASTParams::GetGeneticCodeLabels (vector< string > &labels)   void  CBLASTParams::PrintParams (const string &log_title) const   LOG_POST params for forensic purposes. More...
  string  CBLASTParams::GetLocalNucDB () const   void  CBLASTParams::SetLocalNucDB (const string &value)   string  CBLASTParams::GetLocalProtDB () const   void  CBLASTParams::SetLocalProtDB (const string &value)   ESubjectType  CBLASTParams::GetSubjectType () const   void  CBLASTParams::SetSubjectType (ESubjectType subjectType)   bool  CBLASTParams::GetLocalDBLoader () const   void  CBLASTParams::SetLocalDBLoader (bool value)   void  CBLASTParams::x_AddProgramParams (blast::EProgram program, int thresh, int word, int ev)   void  CBLASTParams::x_ArgsToBlastOptions (const string &cmd_line, blast::CBlastOptions &opts) const   static objects::CUser_object *  CBLASTParams::x_ToUserObject (blast::EProgram prg, const SProgParams &params)   converts SProgParams into CUser_object More...
  static void  CBLASTParams::x_FromUserObject (const objects::CUser_object &user_obj, blast::EProgram prg, SProgParams &params)   reads SProgParams fields from CUser_object More...
    CBLASTSearchParamsPanel::CBLASTSearchParamsPanel ()     CBLASTSearchParamsPanel::CBLASTSearchParamsPanel (wxWindow *parent, wxWindowID id=ID_CBLASTSEARCHPARAMSPANEL, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(), long style=wxTAB_TRAVERSAL)   bool  CBLASTSearchParamsPanel::Create (wxWindow *parent, wxWindowID id=ID_CBLASTSEARCHPARAMSPANEL, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(), long style=wxTAB_TRAVERSAL)     CBLASTSearchParamsPanel::~CBLASTSearchParamsPanel ()   void  CBLASTSearchParamsPanel::Init ()   void  CBLASTSearchParamsPanel::CreateControls ()   bool  CBLASTSearchParamsPanel::TransferDataToWindow ()   bool  CBLASTSearchParamsPanel::TransferDataFromWindow ()   void  CBLASTSearchParamsPanel::OnRepeatTypeSelected (wxCommandEvent &event)   void  CBLASTSearchParamsPanel::OnWindowmaskerTaxIdSelected (wxCommandEvent &event)   void  CBLASTSearchParamsPanel::OnWMDownload (wxCommandEvent &event)   void  CBLASTSearchParamsPanel::OnStandaloneClick (wxCommandEvent &event)   wxString  CBLASTSearchParamsPanel::GetAdvParams () const   void  CBLASTSearchParamsPanel::SetAdvParams (wxString value)   wxString  CBLASTSearchParamsPanel::GetDbGeneticCode () const   void  CBLASTSearchParamsPanel::SetDbGeneticCode (wxString value)   double  CBLASTSearchParamsPanel::GetEValue () const   void  CBLASTSearchParamsPanel::SetEValue (double value)   bool  CBLASTSearchParamsPanel::GetFilterLowComplex () const   void  CBLASTSearchParamsPanel::SetFilterLowComplex (bool value)   wxString  CBLASTSearchParamsPanel::GetJobTitle () const   void  CBLASTSearchParamsPanel::SetJobTitle (wxString value)   wxString  CBLASTSearchParamsPanel::GetGeneticCode () const   void  CBLASTSearchParamsPanel::SetGeneticCode (wxString value)   long  CBLASTSearchParamsPanel::GetThreshold () const   void  CBLASTSearchParamsPanel::SetThreshold (long value)   long  CBLASTSearchParamsPanel::GetWordSize () const   void  CBLASTSearchParamsPanel::SetWordSize (long value)   wxBitmap  CBLASTSearchParamsPanel::GetBitmapResource (const wxString &name)   wxIcon  CBLASTSearchParamsPanel::GetIconResource (const wxString &name)   static bool  CBLASTSearchParamsPanel::ShowToolTips ()   void  CBLASTSearchParamsPanel::SetParams (CBLASTParams *params)   void  CBLASTSearchParamsPanel::x_InitGeneticCodesCombo ()   void  CBLASTSearchParamsPanel::x_HideShowInputs ()   void  CBLASTSearchParamsPanel::x_UpdateMaskCtrls ()   void  CBLASTSearchParamsPanel::x_InitTaxons ()   void  CBLASTSearchParamsPanel::x_ShowWM (bool show)     CBlastSearchTask::CBlastSearchTask (IServiceLocator *srv_locator, CNetBLASTUIDataSource &ds, const string &tool_name)   CBlastSearchTask. More...
  virtual  CBlastSearchTask::~CBlastSearchTask ()   virtual void  CBlastSearchTask::Init_SubmitSearch (const CBLASTParams &params)   setup the task for submitting and monitoring BLAST jobs, and for retrieving results More...
  virtual void  CBlastSearchTask::Init_Monitoring (TDescriptors &descriptors)   setup the task for monitoring BLAST jobs and for retrieving results More...
  virtual void  CBlastSearchTask::Init_RetrieveRID (const vector< string > &RIDs)   setup the task for retrieving results More...
  virtual void  CBlastSearchTask::SetLoadingOptions (CSelectProjectOptions &options)   define how the task results shall be handled More...
  virtual string  CBlastSearchTask::GetStatusText () const   overriding CAppTask::GetStatusText() More...
  void  CBlastSearchTask::x_InitMonitoringStage (TDescriptors &descriptors)   preapres App Job for monitoring stage of the task More...
  void  CBlastSearchTask::x_ReportErrors (vector< string > &errors)     CBLASTSeqToolJob::CBLASTSeqToolJob (const CBLASTParams &params)   static Boolean  CBLASTSeqToolJob::s_BlastInterrupt (SBlastProgress *prog)   static callback for BLAST interruption this must match the API in CBl2Seq and BLAST More...
  virtual void  CBLASTSeqToolJob::RequestCancel ()   RequestCancel() is called to notify the Job that it shall exit Run() function ASAP. More...
  virtual void  CBLASTSeqToolJob::x_CreateProjectItems ()   override this function in derived classes and populate m_Items. More...
  void  CBLASTSeqToolJob::x_CreateProjectItems (vector< CRef< objects::CSeq_align_set > > &aligns)     CBLASTToolManager::CBLASTToolManager ()   CBLASTToolManager. More...
  CRef< CNetBLASTUIDataSource >  CBLASTToolManager::GetBLASTDataSource ()   virtual void  CBLASTToolManager::x_SelectCompatibleInputObjects ()   virtual bool  CBLASTToolManager::x_IsNucInput () const   defines whether Nucleotide or Protein options shall be selected by default More...
  virtual void  CBLASTToolManager::x_CreateOptionsPanelIfNeeded ()   virtual bool  CBLASTToolManager::x_CreateParamsPanelIfNeeded ()   void  CBLASTToolManager::x_InitProjectParams ()   bool  CBLASTToolManager::x_ValidateParams ()   validate parameters after Params page More...
    SCleanupAlignmentsParams::SCleanupAlignmentsParams ()   void  SCleanupAlignmentsParams::Init ()     CCleanupAlignmentsParamsPanel::CCleanupAlignmentsParamsPanel ()     CCleanupAlignmentsParamsPanel::CCleanupAlignmentsParamsPanel (wxWindow *parent, wxWindowID id=ID_CCLEANUPALIGNMENTSPARAMSPANEL, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(400, 300), long style=wxTAB_TRAVERSAL)   bool  CCleanupAlignmentsParamsPanel::Create (wxWindow *parent, wxWindowID id=ID_CCLEANUPALIGNMENTSPARAMSPANEL, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(400, 300), long style=wxTAB_TRAVERSAL)     CCleanupAlignmentsParamsPanel::~CCleanupAlignmentsParamsPanel ()   void  CCleanupAlignmentsParamsPanel::Init ()   void  CCleanupAlignmentsParamsPanel::CreateControls ()   void  CCleanupAlignmentsParamsPanel::SetParams (SCleanupAlignmentsParams *params, TConstScopedObjects *objects)   bool  CCleanupAlignmentsParamsPanel::TransferDataToWindow ()   bool  CCleanupAlignmentsParamsPanel::TransferDataFromWindow ()   virtual void  CCleanupAlignmentsParamsPanel::SetRegistryPath (const string &path)   CAlgoToolManagerParamsPanel. More...
  virtual void  CCleanupAlignmentsParamsPanel::LoadSettings ()   virtual void  CCleanupAlignmentsParamsPanel::SaveSettings () const   override in derived classes More...
  void  CCleanupAlignmentsParamsPanel::OnComboboxSelected (wxCommandEvent &event)   wxBitmap  CCleanupAlignmentsParamsPanel::GetBitmapResource (const wxString &name)   wxIcon  CCleanupAlignmentsParamsPanel::GetIconResource (const wxString &name)   static bool  CCleanupAlignmentsParamsPanel::ShowToolTips ()   void  CCleanupAlignmentsParamsPanel::x_AdjustToAlgoSelector ()   Switch params panel according to current algo-selector. More...
    CCleanupAlignmentsToolManager::CCleanupAlignmentsToolManager ()   void  CCleanupAlignmentsToolManager::x_SelectCompatibleInputObjects ()   select only Seq-aligns More...
  bool  CCleanupAlignmentsToolManager::x_AreSelfAlignmentsOnly () const     CCleanupAlignmentsJob::CCleanupAlignmentsJob (const SCleanupAlignmentsParams &params)   CCleanupAlignmentsJob. More...
  virtual void  CCleanupAlignmentsJob::x_CreateProjectItems ()   override this function in derived classes and populate m_Items. More...
    CClustalOmegaTool::CClustalOmegaTool ()   CClustalOmegaTool. More...
  void  CClustalOmegaTool::x_SelectCompatibleInputObjects ()     CClustalOmegaToolJob::CClustalOmegaToolJob (const CClustalOmegaToolParams &params)   CClustalOmegaToolJob. More...
  virtual wxString  CClustalOmegaToolJob::x_GetCommandLine (const wxString &input, const wxString &output, bool is_nucleotide)   Returns the command line, that will be used to execute the third-party tool. More...
  virtual TConstScopedObjects &  CClustalOmegaToolJob::x_GetObjects ()   Returns the sequences that will be aligned. More...
    CClustalOmegaToolParams::CClustalOmegaToolParams ()     CClustalOmegaToolParams::CClustalOmegaToolParams (const CClustalOmegaToolParams &data)     CClustalOmegaToolParams::~CClustalOmegaToolParams ()   void  CClustalOmegaToolParams::operator= (const CClustalOmegaToolParams &data)   bool  CClustalOmegaToolParams::operator== (const CClustalOmegaToolParams &data) const   void  CClustalOmegaToolParams::Copy (const CClustalOmegaToolParams &data)   void  CClustalOmegaToolParams::Init ()   virtual void  CClustalOmegaToolParams::SetRegistryPath (const string &path)   IRegSettings. More...
  virtual void  CClustalOmegaToolParams::SaveSettings () const   virtual void  CClustalOmegaToolParams::LoadSettings ()   const TConstScopedObjects &  CClustalOmegaToolParams::GetObjects () const   TConstScopedObjects &  CClustalOmegaToolParams::SetObjects ()   wxString  CClustalOmegaToolParams::GetClustalOmegaPath () const   void  CClustalOmegaToolParams::SetClustalOmegaPath (wxString value)   wxString  CClustalOmegaToolParams::GetCommandLine () const   void  CClustalOmegaToolParams::SetCommandLine (wxString value)   bool  CClustalOmegaToolParams::GetGenerateTree () const   void  CClustalOmegaToolParams::SetGenerateTree (bool value)   wxString  CClustalOmegaToolParams::GetClustalOmegaExecutable () const     CClustalwTool::CClustalwTool ()   CClustalwTool. More...
  void  CClustalwTool::x_SelectCompatibleInputObjects ()     CClustalwToolJob::CClustalwToolJob (const CClustalwToolParams &params)   CClustalwToolJob. More...
  virtual wxString  CClustalwToolJob::x_GetCommandLine (const wxString &input, const wxString &output, bool is_nucleotide)   Returns the command line, that will be used to execute the third-party tool. More...
  virtual TConstScopedObjects &  CClustalwToolJob::x_GetObjects ()   Returns the sequences that will be aligned. More...
    CClustalwToolParams::CClustalwToolParams ()     CClustalwToolParams::CClustalwToolParams (const CClustalwToolParams &data)     CClustalwToolParams::~CClustalwToolParams ()   void  CClustalwToolParams::operator= (const CClustalwToolParams &data)   bool  CClustalwToolParams::operator== (const CClustalwToolParams &data) const   void  CClustalwToolParams::Copy (const CClustalwToolParams &data)   void  CClustalwToolParams::Init ()   virtual void  CClustalwToolParams::SetRegistryPath (const string &path)   IRegSettings. More...
  virtual void  CClustalwToolParams::SaveSettings () const   virtual void  CClustalwToolParams::LoadSettings ()   const TConstScopedObjects &  CClustalwToolParams::GetObjects () const   TConstScopedObjects &  CClustalwToolParams::SetObjects ()   wxString  CClustalwToolParams::GetClustalWPath () const   void  CClustalwToolParams::SetClustalWPath (wxString value)   wxString  CClustalwToolParams::GetCommandLine () const   void  CClustalwToolParams::SetCommandLine (wxString value)   bool  CClustalwToolParams::GetGenerateTree () const   void  CClustalwToolParams::SetGenerateTree (bool value)   wxString  CClustalwToolParams::GetClustalWExecutable () const     CCreateGeneModelToolManager::CCreateGeneModelToolManager ()   void  CCreateGeneModelToolManager::x_SelectCompatibleInputObjects ()   void  CCreateGeneModelToolManager::x_RemoveDuplicates ()     SGeneCdsmRnaFeats::SGeneCdsmRnaFeats ()     SGeneCdsmRnaFeats::~SGeneCdsmRnaFeats ()   CConstRef< objects::CSeq_id >  SGeneCdsmRnaFeats::GetID (objects::CScope *scope) const   SGeneCdsmRnaFeats. More...
  void  SGeneCdsmRnaFeats::CrossLinkTriple ()   static void  SGeneCdsmRnaFeats::s_CreateXRefLink (objects::CSeq_feat &from_feat, objects::CSeq_feat &to_feat)   static void  SGeneCdsmRnaFeats::s_CreateDBXref (const objects::CSeq_feat &from_feat, objects::CSeq_feat &to_feat, const string &dbname)     CCreateGeneModelTask::CCreateGeneModelTask (const string &descr, CProjectService *service, CSelectProjectOptions &options, const SCreateGeneModelParams &params)   virtual  CCreateGeneModelTask::~CCreateGeneModelTask ()   static objects::CObject_id::TId  CCreateGeneModelTask::s_GetGeneID (const objects::CSeq_feat &feat)   static objects::CObject_id::TId  CCreateGeneModelTask::s_FindHighestFeatId (const objects::CSeq_entry_Handle seh)   static bool  CCreateGeneModelTask::s_FeaturesHaveIDs (const objects::CSeq_annot &annot)   static bool  CCreateGeneModelTask::s_FeaturesHaveXrefs (const objects::CSeq_annot &annot)   static void  CCreateGeneModelTask::s_AssignFeatureIds (objects::CSeq_annot &annot, objects::CObject_id::TId &max_id)   virtual ETaskState  CCreateGeneModelTask::x_Run ()   override this function in derived classes More...
  CRef< CCmdComposite >  CCreateGeneModelTask::x_GetCommand ()   void  CCreateGeneModelTask::x_StoreGeneratedFeats (const objects::CSeq_annot &annot, TGeneCDSmRNAList &gene_cds_rna) const   void  CCreateGeneModelTask::x_Group_By_GeneID (objects::CSeq_annot &annot, const objects::CSeq_id_Handle &idh)   void  CCreateGeneModelTask::x_GroupGenes (const objects::CSeq_id_Handle &idh, CRef< objects::CSeq_feat > gene)   void  CCreateGeneModelTask::x_AssignIDsAndCrossLinkFeats (objects::CSeq_annot &annot, const objects::CSeq_id_Handle &idh, objects::CObject_id::TId max_id)   CRef< CCmdComposite >  CCreateGeneModelTask::x_AssignIDsAndUpdateGenes (objects::CSeq_annot &annot, const objects::CSeq_id_Handle &idh, objects::CSeq_entry_Handle seh)   void  CCreateGeneModelTask::x_GetUpdatedGeneCommand (objects::CSeq_entry_Handle seh, const objects::CSeq_id_Handle &idh, CCmdComposite *cmd)   bool  CCreateGeneModelTask::x_UpdateGeneOnSequence (TGeneCDSmRNAList &gene_cds_rna, CRef< objects::CSeq_feat > gene)     CCrossAlignView::CCrossAlignView ()   virtual void  CCrossAlignView::x_CreateMenuBarMenu ()   initializes m_MenuBarMenu; override in derived classes More...
  virtual void  CCrossAlignView::x_OnSetSelection (CSelectionEvent &evt)   override in derived classes in order to handle selection broadcast More...
  virtual const CObject *  CCrossAlignView::x_GetOrigObject () const     CDotMatrixView::CDotMatrixView ()   virtual void  CDotMatrixView::x_CreateMenuBarMenu ()   initializes m_MenuBarMenu; override in derived classes More...
  virtual const CObject *  CDotMatrixView::x_GetOrigObject () const   void  CDotMatrixView::x_InitWidget ()     CDotMatrixViewFactory::CDotMatrixViewFactory ()   CDotMatrixViewFactory. More...
    CFindOverlapPanel::CFindOverlapPanel ()     CFindOverlapPanel::CFindOverlapPanel (wxWindow *parent, wxWindowID id=ID_CFINDOVERLAPPANEL, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(400, 300), long style=wxTAB_TRAVERSAL, bool visible=true)   bool  CFindOverlapPanel::Create (wxWindow *parent, wxWindowID id=ID_CFINDOVERLAPPANEL, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(400, 300), long style=wxTAB_TRAVERSAL, bool visible=true)     CFindOverlapPanel::~CFindOverlapPanel ()   void  CFindOverlapPanel::Init ()   void  CFindOverlapPanel::CreateControls ()   virtual bool  CFindOverlapPanel::TransferDataToWindow ()   virtual bool  CFindOverlapPanel::TransferDataFromWindow ()   CFindOverlapParams &  CFindOverlapPanel::GetData ()   const CFindOverlapParams &  CFindOverlapPanel::GetData () const   void  CFindOverlapPanel::SetData (const CFindOverlapParams &data)   wxBitmap  CFindOverlapPanel::GetBitmapResource (const wxString &name)   wxIcon  CFindOverlapPanel::GetIconResource (const wxString &name)   void  CFindOverlapPanel::SetObjects (TConstScopedObjects *objects)   static bool  CFindOverlapPanel::ShowToolTips ()     CFindOverlapParams::CFindOverlapParams ()     CFindOverlapParams::CFindOverlapParams (const CFindOverlapParams &data)     CFindOverlapParams::~CFindOverlapParams ()   void  CFindOverlapParams::operator= (const CFindOverlapParams &data)   bool  CFindOverlapParams::operator== (const CFindOverlapParams &data) const   void  CFindOverlapParams::Copy (const CFindOverlapParams &data)   void  CFindOverlapParams::Init ()   virtual void  CFindOverlapParams::SetRegistryPath (const string &path)   IRegSettings. More...
  virtual void  CFindOverlapParams::SaveSettings () const   IRegSettings. More...
  virtual void  CFindOverlapParams::LoadSettings ()   const SConstScopedObject &  CFindOverlapParams::GetSeq1 () const   SConstScopedObject &  CFindOverlapParams::SetSeq1 ()   const SConstScopedObject &  CFindOverlapParams::GetSeq2 () const   SConstScopedObject &  CFindOverlapParams::SetSeq2 ()   wxString  CFindOverlapParams::GetBlastParams () const   void  CFindOverlapParams::SetBlastParams (wxString value)   int  CFindOverlapParams::GetFilterQuality () const   void  CFindOverlapParams::SetFilterQuality (int value)   wxString  CFindOverlapParams::GetMaxSlop () const   void  CFindOverlapParams::SetMaxSlop (wxString value)     CFindOverlapTool::CFindOverlapTool ()   CFindOverlapTool. More...
  virtual void  CFindOverlapTool::x_SelectCompatibleInputObjects ()   select only Seq-ids More...
    SGroupAlignmentsParams::SGroupAlignmentsParams ()   void  SGroupAlignmentsParams::Init ()     CGroupAlignmentsParamsPanel::CGroupAlignmentsParamsPanel ()     CGroupAlignmentsParamsPanel::CGroupAlignmentsParamsPanel (wxWindow *parent, wxWindowID id=ID_CGROUPALIGNMENTSPARAMSPANEL, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(400, 300), long style=wxTAB_TRAVERSAL)   bool  CGroupAlignmentsParamsPanel::Create (wxWindow *parent, wxWindowID id=ID_CGROUPALIGNMENTSPARAMSPANEL, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(400, 300), long style=wxTAB_TRAVERSAL)     CGroupAlignmentsParamsPanel::~CGroupAlignmentsParamsPanel ()   void  CGroupAlignmentsParamsPanel::Init ()   void  CGroupAlignmentsParamsPanel::CreateControls ()   void  CGroupAlignmentsParamsPanel::SetParams (SGroupAlignmentsParams *params, TConstScopedObjects *objects)   bool  CGroupAlignmentsParamsPanel::TransferDataToWindow ()   bool  CGroupAlignmentsParamsPanel::TransferDataFromWindow ()   wxBitmap  CGroupAlignmentsParamsPanel::GetBitmapResource (const wxString &name)   wxIcon  CGroupAlignmentsParamsPanel::GetIconResource (const wxString &name)   static bool  CGroupAlignmentsParamsPanel::ShowToolTips ()   virtual void  CGroupAlignmentsParamsPanel::SetRegistryPath (const string &path)   CAlgoToolManagerParamsPanel. More...
  virtual void  CGroupAlignmentsParamsPanel::LoadSettings ()   virtual void  CGroupAlignmentsParamsPanel::SaveSettings () const   override in derived classes More...
    CGroupAlignmentsToolManager::CGroupAlignmentsToolManager ()   void  CGroupAlignmentsToolManager::x_SelectCompatibleInputObjects ()   select only Seq-aligns More...
    CGroupAlignmentsJob::CGroupAlignmentsJob (const SGroupAlignmentsParams &params)   CGroupAlignmentsJob. More...
  virtual void  CGroupAlignmentsJob::x_CreateProjectItems ()   override this function in derived classes and populate m_Items. More...
    CKalignTool::CKalignTool ()   CKalignTool. More...
  virtual void  CKalignTool::x_SelectCompatibleInputObjects ()     CKalignToolJob::CKalignToolJob (const CKalignToolParams &params)   CKalignToolJob. More...
  virtual wxString  CKalignToolJob::x_GetCommandLine (const wxString &input, const wxString &output, bool is_nucleotide)   Returns the command line, that will be used to execute the third-party tool. More...
  virtual TConstScopedObjects &  CKalignToolJob::x_GetObjects ()   Returns the sequences that will be aligned. More...
    CKalignToolParams::CKalignToolParams ()     CKalignToolParams::CKalignToolParams (const CKalignToolParams &data)     CKalignToolParams::~CKalignToolParams ()   void  CKalignToolParams::operator= (const CKalignToolParams &data)   bool  CKalignToolParams::operator== (const CKalignToolParams &data) const   void  CKalignToolParams::Copy (const CKalignToolParams &data)   void  CKalignToolParams::Init ()   virtual void  CKalignToolParams::SetRegistryPath (const string &path)   IRegSettings. More...
  virtual void  CKalignToolParams::SaveSettings () const   virtual void  CKalignToolParams::LoadSettings ()   const TConstScopedObjects &  CKalignToolParams::GetObjects () const   TConstScopedObjects &  CKalignToolParams::SetObjects ()   wxString  CKalignToolParams::GetCommandLine () const   void  CKalignToolParams::SetCommandLine (wxString value)   wxString  CKalignToolParams::GetKalignPath () const   void  CKalignToolParams::SetKalignPath (wxString value)   bool  CKalignToolParams::GetQuietFlag () const   void  CKalignToolParams::SetQuietFlag (bool value)   wxString  CKalignToolParams::GetKalignExecutable () const     CMafftTool::CMafftTool ()   CMafftTool. More...
  virtual void  CMafftTool::x_SelectCompatibleInputObjects ()     CMafftToolJob::CMafftToolJob (const CMafftToolParams &params)   CMafftToolJob. More...
  virtual wxString  CMafftToolJob::x_GetCommandLine (const wxString &input, const wxString &output, bool is_nucleotide)   Returns the command line, that will be used to execute the third-party tool. More...
  virtual TConstScopedObjects &  CMafftToolJob::x_GetObjects ()   Returns the sequences that will be aligned. More...
  virtual wxString  CMafftToolJob::x_GetWorkingDirectory () const   Returns the directory where to execute the msa tool. More...
    CMafftToolParams::CMafftToolParams ()     CMafftToolParams::CMafftToolParams (const CMafftToolParams &data)     CMafftToolParams::~CMafftToolParams ()   void  CMafftToolParams::operator= (const CMafftToolParams &data)   bool  CMafftToolParams::operator== (const CMafftToolParams &data) const   void  CMafftToolParams::Copy (const CMafftToolParams &data)   void  CMafftToolParams::Init ()   virtual void  CMafftToolParams::SetRegistryPath (const string &path)   IRegSettings. More...
  virtual void  CMafftToolParams::SaveSettings () const   virtual void  CMafftToolParams::LoadSettings ()   const TConstScopedObjects &  CMafftToolParams::GetObjects () const   TConstScopedObjects &  CMafftToolParams::SetObjects ()   bool  CMafftToolParams::GetAutoFlag () const   void  CMafftToolParams::SetAutoFlag (bool value)   wxString  CMafftToolParams::GetCommandLine () const   void  CMafftToolParams::SetCommandLine (wxString value)   wxString  CMafftToolParams::GetMafftPath () const   void  CMafftToolParams::SetMafftPath (wxString value)   bool  CMafftToolParams::GetQuietFlag () const   void  CMafftToolParams::SetQuietFlag (bool value)   wxString  CMafftToolParams::GetMafftExecutable () const     SMergeAlignmentsParams::SMergeAlignmentsParams ()   SMergeAlignmentsParams. More...
  void  SMergeAlignmentsParams::Init ()     CMergeAlignmentsParamsPanel::CMergeAlignmentsParamsPanel ()   CMergeAlignmentsParamsPanel. More...
    CMergeAlignmentsParamsPanel::CMergeAlignmentsParamsPanel (wxWindow *parent, wxWindowID id=ID_CBLASTSEARCHOPTIONSPANEL, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(400, 300), long style=wxTAB_TRAVERSAL)   bool  CMergeAlignmentsParamsPanel::Create (wxWindow *parent, wxWindowID id=ID_CBLASTSEARCHOPTIONSPANEL, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(400, 300), long style=wxTAB_TRAVERSAL)     CMergeAlignmentsParamsPanel::~CMergeAlignmentsParamsPanel ()   void  CMergeAlignmentsParamsPanel::Init ()   void  CMergeAlignmentsParamsPanel::CreateControls ()   bool  CMergeAlignmentsParamsPanel::TransferDataToWindow ()   bool  CMergeAlignmentsParamsPanel::TransferDataFromWindow ()   wxBitmap  CMergeAlignmentsParamsPanel::GetBitmapResource (const wxString &name)   wxIcon  CMergeAlignmentsParamsPanel::GetIconResource (const wxString &name)   static bool  CMergeAlignmentsParamsPanel::ShowToolTips ()   void  CMergeAlignmentsParamsPanel::SetParams (SMergeAlignmentsParams *params, TConstScopedObjects *objects)   virtual void  CMergeAlignmentsParamsPanel::SetRegistryPath (const string &path)   CAlgoToolManagerParamsPanel. More...
  virtual void  CMergeAlignmentsParamsPanel::LoadSettings ()   virtual void  CMergeAlignmentsParamsPanel::SaveSettings () const   override in derived classes More...
    CMergeAlignmentsToolManager::CMergeAlignmentsToolManager ()   CMergeAlignmentsToolManager. More...
  void  CMergeAlignmentsToolManager::x_SelectCompatibleInputObjects ()   select only Seq-aligns More...
    CMergeAlignmentsJob::CMergeAlignmentsJob (const SMergeAlignmentsParams &params)   CMergeAlignmentsJob. More...
  virtual void  CMergeAlignmentsJob::x_CreateProjectItems ()   override this function in derived classes and populate m_Items. More...
    CMPCrossAlignView::CMPCrossAlignView ()   virtual void  CMPCrossAlignView::x_CreateMenuBarMenu ()   initializes m_MenuBarMenu; override in derived classes More...
  virtual void  CMPCrossAlignView::x_OnSetSelection (CSelectionEvent &evt)   override in derived classes in order to handle selection broadcast More...
  const CObject *  CMPCrossAlignView::x_GetOrigObject () const     CMSAToolJob::CMSAToolJob (const wxString &tool_name)   CMSAToolJob. More...
  virtual  CMSAToolJob::~CMSAToolJob ()   virtual bool  CMSAToolJob::BeforeRun ()   Function will be called on the main thread before execution of Run Should not do any lengthy work returns true to continue job execution on worker thread false to quit execution with status - failed. More...
  virtual void  CMSAToolJob::x_CreateProjectItems ()   override this function in derived classes and populate m_Items. More...
  virtual void  CMSAToolJob::x_AddTreeProjectItem (const string &title, const string &comment)   virtual wxString  CMSAToolJob::x_GetCommandLine (const wxString &input, const wxString &output, bool is_nucleotide)=0   Returns the command line, that will be used to execute the third-party tool. More...
  virtual TConstScopedObjects &  CMSAToolJob::x_GetObjects ()=0   Returns the sequences that will be aligned. More...
  virtual wxString  CMSAToolJob::x_GetWorkingDirectory () const   Returns the directory where to execute the msa tool. More...
    CMultiAlignView::DECLARE_EVENT_MAP ()     CMultiAlignView::CMultiAlignView ()   void  CMultiAlignView::OnAlnWidgetSelChanged (CEvent *evt)   void  CMultiAlignView::OnOpenGraphicalView (CEvent *evt)   virtual void  CMultiAlignView::x_CreateMenuBarMenu ()   initializes m_MenuBarMenu; override in derived classes More...
  virtual const SwxMenuItemRec *  CMultiAlignView::GetMenuDef () const   simpler way to provide a static menu using macros defined earlier in this file More...
  virtual bool  CMultiAlignView::x_GetValidInputData (const CObject *obj)   virtual void  CMultiAlignView::x_RebuildObjectIndex ()   virtual void  CMultiAlignView::x_GetRowSeqLoc (CAlnVec::TNumrow row, CSelectionEvent::TRangeColl &loc) const   virtual bool  CMultiAlignView::x_GetSeqRangeSelection (CAlnMultiWidget::TRangeColl &seq_coll) const   virtual void  CMultiAlignView::x_OnSetSelection (CSelectionEvent &evt)   override in derived classes in order to handle selection broadcast More...
  virtual const CObject *  CMultiAlignView::x_GetOrigObject () const   virtual bool  CMultiAlignView::x_MergeObjects (TConstScopedObjects &objects)     CMultiAlignViewFactory::CMultiAlignViewFactory ()   bool  CMultiAlignViewFactory::x_NeedsConversion (const CObject &object, objects::CScope &scope)     CSelRowHandle::CSelRowHandle (IAlnExplorer::TNumrow row)   IAlnExplorer::TNumrow  CSelRowHandle::GetNumrow () const     CMuscleTool::CMuscleTool ()   CMuscleTool. More...
  virtual void  CMuscleTool::x_SelectCompatibleInputObjects ()     CMuscleToolJob::CMuscleToolJob (const CMuscleToolParams &params)   CMuscleToolJob. More...
  virtual wxString  CMuscleToolJob::x_GetCommandLine (const wxString &input, const wxString &output, bool is_nucleotide)   Returns the command line, that will be used to execute the third-party tool. More...
  virtual TConstScopedObjects &  CMuscleToolJob::x_GetObjects ()   Returns the sequences that will be aligned. More...
    CMuscleToolParams::CMuscleToolParams ()     CMuscleToolParams::CMuscleToolParams (const CMuscleToolParams &data)     CMuscleToolParams::~CMuscleToolParams ()   void  CMuscleToolParams::operator= (const CMuscleToolParams &data)   bool  CMuscleToolParams::operator== (const CMuscleToolParams &data) const   void  CMuscleToolParams::Copy (const CMuscleToolParams &data)   void  CMuscleToolParams::Init ()   virtual void  CMuscleToolParams::SetRegistryPath (const string &path)   IRegSettings. More...
  virtual void  CMuscleToolParams::SaveSettings () const   virtual void  CMuscleToolParams::LoadSettings ()   const TConstScopedObjects &  CMuscleToolParams::GetObjects () const   TConstScopedObjects &  CMuscleToolParams::SetObjects ()   wxString  CMuscleToolParams::GetCommandLine () const   void  CMuscleToolParams::SetCommandLine (wxString value)   bool  CMuscleToolParams::GetGenerateTree () const   void  CMuscleToolParams::SetGenerateTree (bool value)   wxString  CMuscleToolParams::GetMusclePath () const   void  CMuscleToolParams::SetMusclePath (wxString value)   int  CMuscleToolParams::GetScoringMethod () const   void  CMuscleToolParams::SetScoringMethod (int value)   wxString  CMuscleToolParams::GetMuscleExecutable () const     CNeedlemanWunschToolParams::CNeedlemanWunschToolParams ()     CNeedlemanWunschToolParams::CNeedlemanWunschToolParams (const CNeedlemanWunschToolParams &data)     CNeedlemanWunschToolParams::~CNeedlemanWunschToolParams ()   void  CNeedlemanWunschToolParams::operator= (const CNeedlemanWunschToolParams &data)   bool  CNeedlemanWunschToolParams::operator== (const CNeedlemanWunschToolParams &data) const   void  CNeedlemanWunschToolParams::Copy (const CNeedlemanWunschToolParams &data)   void  CNeedlemanWunschToolParams::Init ()   virtual void  CNeedlemanWunschToolParams::SetRegistryPath (const string &path)   IRegSettings. More...
  virtual void  CNeedlemanWunschToolParams::SaveSettings () const   virtual void  CNeedlemanWunschToolParams::LoadSettings ()   const TConstScopedObjects &  CNeedlemanWunschToolParams::GetObjects () const   TConstScopedObjects &  CNeedlemanWunschToolParams::SetObjects ()   int  CNeedlemanWunschToolParams::GetBandSize () const   void  CNeedlemanWunschToolParams::SetBandSize (int value)   int  CNeedlemanWunschToolParams::GetFirstSeqFreeEnds () const   void  CNeedlemanWunschToolParams::SetFirstSeqFreeEnds (int value)   int  CNeedlemanWunschToolParams::GetGapExtendCost () const   void  CNeedlemanWunschToolParams::SetGapExtendCost (int value)   int  CNeedlemanWunschToolParams::GetGapOpenCost () const   void  CNeedlemanWunschToolParams::SetGapOpenCost (int value)   int  CNeedlemanWunschToolParams::GetMatchCost () const   void  CNeedlemanWunschToolParams::SetMatchCost (int value)   int  CNeedlemanWunschToolParams::GetMismatchCost () const   void  CNeedlemanWunschToolParams::SetMismatchCost (int value)   int  CNeedlemanWunschToolParams::GetSecondSeqFreeEnds () const   void  CNeedlemanWunschToolParams::SetSecondSeqFreeEnds (int value)     CNetBlastDMSearchFormPanel::CNetBlastDMSearchFormPanel ()     CNetBlastDMSearchFormPanel::CNetBlastDMSearchFormPanel (wxWindow *parent, wxWindowID id=ID_CNETBLASTDMSEARCHFORM, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxDefaultSize, long style=wxTAB_TRAVERSAL)   bool  CNetBlastDMSearchFormPanel::Create (wxWindow *parent, wxWindowID id=ID_CNETBLASTDMSEARCHFORM, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxDefaultSize, long style=wxTAB_TRAVERSAL)     CNetBlastDMSearchFormPanel::~CNetBlastDMSearchFormPanel ()   void  CNetBlastDMSearchFormPanel::Init ()   void  CNetBlastDMSearchFormPanel::CreateControls ()   bool  CNetBlastDMSearchFormPanel::TransferDataToWindow ()   void  CNetBlastDMSearchFormPanel::OnFilterInputTextUpdated (wxCommandEvent &event)   void  CNetBlastDMSearchFormPanel::OnResetClick (wxCommandEvent &event)   void  CNetBlastDMSearchFormPanel::OnSubmittedCheckClick (wxCommandEvent &event)   bool  CNetBlastDMSearchFormPanel::GetCompleted () const   void  CNetBlastDMSearchFormPanel::SetCompleted (bool value)   bool  CNetBlastDMSearchFormPanel::GetSubmitted () const   void  CNetBlastDMSearchFormPanel::SetSubmitted (bool value)   bool  CNetBlastDMSearchFormPanel::GetFailed () const   void  CNetBlastDMSearchFormPanel::SetFailed (bool value)   bool  CNetBlastDMSearchFormPanel::GetRetrieved () const   void  CNetBlastDMSearchFormPanel::SetRetrieved (bool value)   bool  CNetBlastDMSearchFormPanel::GetExpired () const   void  CNetBlastDMSearchFormPanel::SetExpired (bool value)   wxString  CNetBlastDMSearchFormPanel::GetSearchValue () const   void  CNetBlastDMSearchFormPanel::SetSearchValue (wxString value)   wxBitmap  CNetBlastDMSearchFormPanel::GetBitmapResource (const wxString &name)   wxIcon  CNetBlastDMSearchFormPanel::GetIconResource (const wxString &name)   static bool  CNetBlastDMSearchFormPanel::ShowToolTips ()   void  CNetBlastDMSearchFormPanel::RestartSearch ()     CNetBLAST_DMSearchTool::CNetBLAST_DMSearchTool ()   IDMSearchTool. More...
  void  CNetBLAST_DMSearchTool::GetDbNames (vector< string > &name)   virtual IDMSearchTool::TUIToolFlags  CNetBLAST_DMSearchTool::GetFlags (void)   special flags More...
  virtual CRef< CSearchJobBase >  CNetBLAST_DMSearchTool::x_CreateJob (IDMSearchQuery &query)   implementing CSearchToolBase pure virtual function More...
  CNetBLASTUIDataSource *  CNetBLAST_DMSearchTool::x_GetDataSource ()     CNetBLAST_DMSearchQuery::CNetBLAST_DMSearchQuery (const TStates &states, const string &filter_str)   CNetBLAST_DMSearchQuery. More...
  virtual string  CNetBLAST_DMSearchQuery::ToString () const   Prepare a string representation of a query (for logging and debugging) More...
    CNetBLAST_DMSearchForm::DECLARE_EVENT_MAP ()     CNetBLAST_DMSearchForm::CNetBLAST_DMSearchForm (CNetBLAST_DMSearchTool &tool)   CNetBLAST_DMSearchForm. More...
  virtual  CNetBLAST_DMSearchForm::~CNetBLAST_DMSearchForm ()   void  CNetBLAST_DMSearchForm::SetDataSource (CNetBLASTUIDataSource *dataSource)   void  CNetBLAST_DMSearchForm::x_OnJobDescrChanged (CEvent *)   virtual void  CNetBLAST_DMSearchForm::x_LoadSettings (const CRegistryReadView &view)   virtual void  CNetBLAST_DMSearchForm::x_SaveSettings (CRegistryWriteView view) const   IDMSearchTool *  CNetBLAST_DMSearchForm::x_GetTool (void)     CNetBLAST_DMSearchJob::CNetBLAST_DMSearchJob (CNetBLAST_DMSearchQuery &query, CNetBLASTUIDataSource &ds)   CNetBLAST_DMSearchJob. More...
  static string  CNetBlastJobDescriptor::GetStateLabel (EState state)   virtual  CNetBlastJobDescriptor::~CNetBlastJobDescriptor ()   EState  CNetBlastJobDescriptor::GetState () const   string  CNetBlastJobDescriptor::GetRID () const   string  CNetBlastJobDescriptor::GetJobTitle () const   string  CNetBlastJobDescriptor::GetDescription () const   string  CNetBlastJobDescriptor::GetErrors () const   time_t  CNetBlastJobDescriptor::GetSubmitTime () const   void  CNetBlastJobDescriptor::Init (const CBLASTParams &params, CNetBLASTUIDataSource &ds)   void  CNetBlastJobDescriptor::Init (const string &rid, CNetBLASTUIDataSource &ds)   void  CNetBlastJobDescriptor::Submit (objects::CBioseq_set &seq_set)   void  CNetBlastJobDescriptor::Check ()   CRef< objects::CSeq_align_set >  CNetBlastJobDescriptor::Retrieve ()   CRef< blast::CRemoteBlast >  CNetBlastJobDescriptor::GetRemoteBlast ()   void  CNetBlastJobDescriptor::Release ()   release CRemoteBlast object to free associated resources More...
  void  CNetBlastJobDescriptor::MarkDeleted (bool deleted)   bool  CNetBlastJobDescriptor::IsDeleted () const   objects::CUser_object *  CNetBlastJobDescriptor::ToUserObject () const   void  CNetBlastJobDescriptor::FromUserObject (const objects::CUser_object &user_obj)     CNetBlastJobDescriptor::CNetBlastJobDescriptor ()   CNetBlastJobDescriptor. More...
    CNetBlastJobDescriptor::CNetBlastJobDescriptor (CNetBLASTUIDataSource &ds)     CNetBlastJobDescriptor::CNetBlastJobDescriptor (const CNetBlastJobDescriptor &)   CNetBlastJobDescriptor &  CNetBlastJobDescriptor::operator= (const CNetBlastJobDescriptor &)   void  CNetBlastJobDescriptor::x_CreateRemoteBlastIfNeeded ()   void  CNetBlastJobDescriptor::x_NotifyDataSource ()     CNetBLASTLoadOptionPanel::CNetBLASTLoadOptionPanel ()     CNetBLASTLoadOptionPanel::CNetBLASTLoadOptionPanel (wxWindow *parent, wxWindowID id=ID_NETBLASTLOADOPTIONPANEL, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(400, 300), long style=wxTAB_TRAVERSAL)   bool  CNetBLASTLoadOptionPanel::Create (wxWindow *parent, wxWindowID id=ID_NETBLASTLOADOPTIONPANEL, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(400, 300), long style=wxTAB_TRAVERSAL)     CNetBLASTLoadOptionPanel::~CNetBLASTLoadOptionPanel ()   void  CNetBLASTLoadOptionPanel::Init ()   void  CNetBLASTLoadOptionPanel::CreateControls ()   wxBitmap  CNetBLASTLoadOptionPanel::GetBitmapResource (const wxString &name)   wxIcon  CNetBLASTLoadOptionPanel::GetIconResource (const wxString &name)   static bool  CNetBLASTLoadOptionPanel::ShowToolTips ()   string  CNetBLASTLoadOptionPanel::GetInput () const   void  CNetBLASTLoadOptionPanel::SetInput (const string &input)   bool  CNetBLASTLoadOptionPanel::IsInputValid ()   void  CNetBLASTLoadOptionPanel::GetRIDs (vector< string > &rids)     CNetBLASTUIDataSourceEvent::CNetBLASTUIDataSourceEvent ()     CNetBLASTUIDataSource::CNetBLASTUIDataSource (CNetBLASTUIDataSourceType &type)   virtual  CNetBLASTUIDataSource::~CNetBLASTUIDataSource ()   void  CNetBLASTUIDataSource::x_SaveJobDescriptors ()   void  CNetBLASTUIDataSource::x_LoadJobDescriptors ()   void  CNetBLASTUIDataSource::x_OnJobDescrChanged (CNetBlastJobDescriptor &descr)   callback - invoked by CNetBlastJobDescriptor More...
  void  CNetBLASTUIDataSource::x_StartTask (CBlastSearchTask &task)   void  CNetBLASTUIDataSource::x_AutoStartMonitoring ()     CNetBLASTUIDataSourceType::CNetBLASTUIDataSourceType ()   CNetBLASTUIDataSourceType. More...
    CNetBLASTUILoadManager::CNetBLASTUILoadManager (CNetBLASTUIDataSource &data_source)   CNetBLASTUILoadManager. More...
    CNGAlignJob::CNGAlignJob (const CNGAlignParams &params)   CNGAlignJob. More...
  virtual void  CNGAlignJob::x_CreateProjectItems ()   override this function in derived classes and populate m_Items. More...
    CNGAlignParams::CNGAlignParams ()     CNGAlignParams::CNGAlignParams (const CNGAlignParams &data)     CNGAlignParams::~CNGAlignParams ()   void  CNGAlignParams::operator= (const CNGAlignParams &data)   bool  CNGAlignParams::operator== (const CNGAlignParams &data) const   void  CNGAlignParams::Copy (const CNGAlignParams &data)   void  CNGAlignParams::Init ()   virtual void  CNGAlignParams::SetRegistryPath (const string &path)   IRegSettings. More...
  virtual void  CNGAlignParams::SaveSettings () const   virtual void  CNGAlignParams::LoadSettings ()   const SConstScopedObject &  CNGAlignParams::GetSubject () const   SConstScopedObject &  CNGAlignParams::SetSubject ()   const TConstScopedObjects &  CNGAlignParams::GetQueries () const   TConstScopedObjects &  CNGAlignParams::SetQueries ()   int  CNGAlignParams::GetFilterMode () const   void  CNGAlignParams::SetFilterMode (int value)   long  CNGAlignParams::GetWordSize () const   void  CNGAlignParams::SetWordSize (long value)   double  CNGAlignParams::GetEValue () const   void  CNGAlignParams::SetEValue (double value)   bool  CNGAlignParams::GetBestHit () const   void  CNGAlignParams::SetBestHit (bool value)   wxString  CNGAlignParams::GetJobTitle () const   void  CNGAlignParams::SetJobTitle (wxString value)   wxString  CNGAlignParams::GetAdvParams () const   void  CNGAlignParams::SetAdvParams (wxString value)   int  CNGAlignParams::GetWMTaxId () const   void  CNGAlignParams::SetWMTaxId (int value)   string  CNGAlignParams::GetWMDir () const   void  CNGAlignParams::SetWMDir (string value)   void  CNGAlignParams::LogDump ()     CNGAlignTool::CNGAlignTool ()   CNGAlignTool. More...
  void  CNGAlignTool::x_CreateBALSTPanelIfNeeded ()   virtual void  CNGAlignTool::x_SelectCompatibleInputObjects ()   wxPanel *  CNGAlignTool::x_GetCurrentPage ()   bool  CNGAlignTool::x_IsFirstPage () const   bool  CNGAlignTool::x_IsLastPage () const   bool  CNGAlignTool::x_GoFirstPage ()   bool  CNGAlignTool::x_GoNextPage ()   bool  CNGAlignTool::x_GoPrevPage ()   bool  CNGAlignTool::x_GoLastPage ()   bool  CNGAlignTool::x_LoadPage ()     CPhyTreeView::DECLARE_EVENT_MAP ()     CPhyTreeView::CPhyTreeView ()     CPhyTreeView::~CPhyTreeView ()   CRef< CPhyloTreeScheme >  CPhyTreeView::GetScheme ()   CPhyloTreeWidget *  CPhyTreeView::GetWidget () const   void  CPhyTreeView::OnBioTreeChanged ()   void  CPhyTreeView::OnExportTree (CEvent *evt)   void  CPhyTreeView::OnSomethingEdited (CEvent *evt)   void  CPhyTreeView::OnCreateSelectedSubtree (CEvent *evt)   void  CPhyTreeView::CommitTheChanges (CNcbiIstrstream &istr)   void  CPhyTreeView::AppliedEditToDataSource ()   void  CPhyTreeView::RebuildObjectIndex ()   virtual void  CPhyTreeView::x_CreateMenuBarMenu ()   initializes m_MenuBarMenu; override in derived classes More...
  virtual void  CPhyTreeView::x_OnSetSelection (CSelectionEvent &evt)   override in derived classes in order to handle selection broadcast More...
  virtual const CObject *  CPhyTreeView::x_GetOrigObject () const   void  CPhyTreeView::x_QueryStatusChange (CEvent *evt)     CPhyloTreeJob::CPhyloTreeJob (const objects::CBioTreeContainer *btc)   virtual void  CPhyloTreeJob::x_CreateProjectItems ()   override this function in derived classes and populate m_Items. More...
    CProSplignTool::CProSplignTool ()   CProSplignTool. More...
  virtual void  CProSplignTool::x_SelectCompatibleInputObjects ()     CMolTypeValidator::CMolTypeValidator (MolType molType)   virtual CConstRef< CObject >  CMolTypeValidator::Validate (const objects::CSeq_id &id, objects::CScope &scope, wxString &errMessage)     CSplignPanel::CSplignPanel ()     CSplignPanel::CSplignPanel (wxWindow *parent, wxWindowID id=ID_CSPLIGNPANEL, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(400, 300), long style=wxCLIP_CHILDREN|wxTAB_TRAVERSAL, bool visibale=true)   bool  CSplignPanel::Create (wxWindow *parent, wxWindowID id=ID_CSPLIGNPANEL, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(400, 300), long style=wxCLIP_CHILDREN|wxTAB_TRAVERSAL, bool visibale=true)     CSplignPanel::~CSplignPanel ()   void  CSplignPanel::Init ()   void  CSplignPanel::CreateControls ()   virtual bool  CSplignPanel::TransferDataFromWindow ()   SConstScopedObject  CSplignPanel::GetGenomicSeq () const   void  CSplignPanel::SetGenomicSeq (SConstScopedObject value)   TConstScopedObjects  CSplignPanel::GetCDNASeqs () const   void  CSplignPanel::SetCDNASeqs (TConstScopedObjects value)   CSplignParams &  CSplignPanel::GetData ()   const CSplignParams &  CSplignPanel::GetData () const   void  CSplignPanel::SetData (const CSplignParams &data)   wxBitmap  CSplignPanel::GetBitmapResource (const wxString &name)   wxIcon  CSplignPanel::GetIconResource (const wxString &name)   void  CSplignPanel::SetObjects (map< string, TConstScopedObjects > *genomic, map< string, TConstScopedObjects > *na)   static bool  CSplignPanel::ShowToolTips ()     CSplignParams::CSplignParams ()     CSplignParams::CSplignParams (const CSplignParams &data)     CSplignParams::~CSplignParams ()   void  CSplignParams::operator= (const CSplignParams &data)   bool  CSplignParams::operator== (const CSplignParams &data) const   void  CSplignParams::Copy (const CSplignParams &data)   void  CSplignParams::Init ()   virtual void  CSplignParams::SetRegistryPath (const string &path)   IRegSettings. More...
  virtual void  CSplignParams::SaveSettings () const   virtual void  CSplignParams::LoadSettings ()   double  CSplignParams::GetCompPenalty () const   void  CSplignParams::SetCompPenalty (double value)   int  CSplignParams::GetDiscType () const   void  CSplignParams::SetDiscType (int value)   bool  CSplignParams::GetEndGapDetect () const   void  CSplignParams::SetEndGapDetect (bool value)   long  CSplignParams::GetMaxGenomicExtent () const   void  CSplignParams::SetMaxGenomicExtent (long value)   long  CSplignParams::GetMaxIntron () const   void  CSplignParams::SetMaxIntron (long value)   double  CSplignParams::GetMinCompIdentity () const   void  CSplignParams::SetMinCompIdentity (double value)   double  CSplignParams::GetMinExonIdentity () const   void  CSplignParams::SetMinExonIdentity (double value)   bool  CSplignParams::GetPolyADetect () const   void  CSplignParams::SetPolyADetect (bool value)   int  CSplignParams::GetCDNAStrand () const   void  CSplignParams::SetCDNAStrand (int value)   virtual void  CSplignParams::DebugDump (CDebugDumpContext ddc, unsigned int depth) const     CSplignTool::CSplignTool ()   CSplignTool. More...
  virtual void  CSplignTool::x_SelectCompatibleInputObjects ()     CCommonTaxTreeTool::CCommonTaxTreeTool ()   CCommonTaxTreeTool. More...
  void  CCommonTaxTreeTool::x_SelectCompatibleInputObjects ()     CTaxTreeToolJob::CTaxTreeToolJob (const CTaxTreeToolParams &params)   CTaxTreeToolJob. More...
  virtual void  CTaxTreeToolJob::x_CreateProjectItems ()   override this function in derived classes and populate m_Items. More...
    CTaxTreeToolParams::CTaxTreeToolParams ()     CTaxTreeToolParams::CTaxTreeToolParams (const CTaxTreeToolParams &data)     CTaxTreeToolParams::~CTaxTreeToolParams ()   void  CTaxTreeToolParams::operator= (const CTaxTreeToolParams &data)   bool  CTaxTreeToolParams::operator== (const CTaxTreeToolParams &data) const   void  CTaxTreeToolParams::Copy (const CTaxTreeToolParams &data)   void  CTaxTreeToolParams::Init ()   virtual void  CTaxTreeToolParams::SetRegistryPath (const string &path)   IRegSettings. More...
  virtual void  CTaxTreeToolParams::SaveSettings () const   virtual void  CTaxTreeToolParams::LoadSettings ()   const TConstScopedObjects &  CTaxTreeToolParams::GetObjects () const   TConstScopedObjects &  CTaxTreeToolParams::SetObjects ()     CTreeBuilderPanel::CTreeBuilderPanel ()     CTreeBuilderPanel::CTreeBuilderPanel (wxWindow *parent, wxWindowID id=ID_CTreeBuilderPanel, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(400, 300), long style=wxTAB_TRAVERSAL)   bool  CTreeBuilderPanel::Create (wxWindow *parent, wxWindowID id=ID_CTreeBuilderPanel, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(400, 300), long style=wxTAB_TRAVERSAL)     CTreeBuilderPanel::~CTreeBuilderPanel ()   void  CTreeBuilderPanel::Init ()   void  CTreeBuilderPanel::CreateControls ()   virtual bool  CTreeBuilderPanel::TransferDataToWindow ()   virtual bool  CTreeBuilderPanel::TransferDataFromWindow ()   CTreeBuilderParams &  CTreeBuilderPanel::GetData ()   const CTreeBuilderParams &  CTreeBuilderPanel::GetData () const   void  CTreeBuilderPanel::SetData (const CTreeBuilderParams &data)   wxBitmap  CTreeBuilderPanel::GetBitmapResource (const wxString &name)   wxIcon  CTreeBuilderPanel::GetIconResource (const wxString &name)   void  CTreeBuilderPanel::SetObjects (TConstScopedObjects *objects)   static bool  CTreeBuilderPanel::ShowToolTips ()     CTreeBuilderParams::CTreeBuilderParams ()     CTreeBuilderParams::CTreeBuilderParams (const CTreeBuilderParams &data)     CTreeBuilderParams::~CTreeBuilderParams ()   void  CTreeBuilderParams::operator= (const CTreeBuilderParams &data)   bool  CTreeBuilderParams::operator== (const CTreeBuilderParams &data) const   void  CTreeBuilderParams::Copy (const CTreeBuilderParams &data)   void  CTreeBuilderParams::Init ()   virtual void  CTreeBuilderParams::SetRegistryPath (const string &path)   IRegSettings. More...
  virtual void  CTreeBuilderParams::SaveSettings () const   IRegSettings. More...
  virtual void  CTreeBuilderParams::LoadSettings ()   const SConstScopedObject &  CTreeBuilderParams::GetObject () const   SConstScopedObject &  CTreeBuilderParams::SetObject ()   wxString  CTreeBuilderParams::GetDistanceMethod () const   void  CTreeBuilderParams::SetDistanceMethod (wxString value)   wxString  CTreeBuilderParams::GetConstructMethod () const   void  CTreeBuilderParams::SetConstructMethod (wxString value)   wxString  CTreeBuilderParams::GetLeafLabels () const   void  CTreeBuilderParams::SetLeafLabels (wxString value)     CTreeBuilderTool::CTreeBuilderTool ()   CTreeBuilderTool. More...
  virtual void  CTreeBuilderTool::x_SelectCompatibleInputObjects ()   select only Seq-ids More...
    CDebugMacroToolJob::CDebugMacroToolJob (const CDebugMacroToolParams &params)   CDebugMacroToolJob. More...
  virtual void  CDebugMacroToolJob::x_CreateProjectItems ()   override this function in derived classes and populate m_Items. More...
    CTextAlignObjectLoader::CTextAlignObjectLoader (const CTextAlignParams &params)     CTextAlignObjectLoader::CTextAlignObjectLoader (const CTextAlignParams &params, const vector< wxString > &filenames)   void  CTextAlignObjectLoader::Init ()   void  CTextAlignObjectLoader::LoadFromStream (CNcbiIstream &istr, TObjects &objects, string &errMsg)     CAdvancedCleanupTool::CAdvancedCleanupTool ()   CAdvancedCleanupTool. More...
  virtual void  CAdvancedCleanupTool::x_SelectCompatibleInputObjects ()     CCreateNeedlemanWunschToolManager::CCreateNeedlemanWunschToolManager ()   void  CCreateNeedlemanWunschToolManager::x_SelectCompatibleInputObjects ()   select only Seq-aligns More...
    CCreateNeedlemanWunschJob::CCreateNeedlemanWunschJob (const CNeedlemanWunschToolParams &params)   CCreateNeedlemanWunschJob. More...
  bool  CCreateNeedlemanWunschJob::ProgressCallback (const string &status, float done)   virtual CConstIRef< IAppJobProgress >  CCreateNeedlemanWunschJob::GetProgress ()   implement Run() in derived classes, make sure that exceptions are handled and m_StopRequested flag is respected. More...
  virtual void  CCreateNeedlemanWunschJob::x_CreateProjectItems ()   override this function in derived classes and populate m_Items. More...
    CMuscleToolPanel::CMuscleToolPanel ()     CMuscleToolPanel::CMuscleToolPanel (wxWindow *parent, wxWindowID id=ID_CMUSCLEPANEL, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(400, 300), long style=wxTAB_TRAVERSAL, bool visible=true)   bool  CMuscleToolPanel::Create (wxWindow *parent, wxWindowID id=ID_CMUSCLEPANEL, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(400, 300), long style=wxTAB_TRAVERSAL, bool visible=true)     CMuscleToolPanel::~CMuscleToolPanel ()   void  CMuscleToolPanel::Init ()   void  CMuscleToolPanel::CreateControls ()   virtual bool  CMuscleToolPanel::TransferDataFromWindow ()   void  CMuscleToolPanel::OnMusclePathClick (wxCommandEvent &event)   CMuscleToolParams &  CMuscleToolPanel::GetData ()   const CMuscleToolParams &  CMuscleToolPanel::GetData () const   void  CMuscleToolPanel::SetData (const CMuscleToolParams &data)   wxBitmap  CMuscleToolPanel::GetBitmapResource (const wxString &name)   wxIcon  CMuscleToolPanel::GetIconResource (const wxString &name)   void  CMuscleToolPanel::SetObjects (map< string, TConstScopedObjects > *objects)   static bool  CMuscleToolPanel::ShowToolTips ()     CNGAlignPanel::CNGAlignPanel ()     CNGAlignPanel::CNGAlignPanel (wxWindow *parent)   bool  CNGAlignPanel::Create (wxWindow *parent, wxWindowID id=ID_CNGALIGNPANEL)     CNGAlignPanel::~CNGAlignPanel ()   void  CNGAlignPanel::Init ()   void  CNGAlignPanel::CreateControls ()   virtual bool  CNGAlignPanel::TransferDataFromWindow ()   const SConstScopedObject &  CNGAlignPanel::GetSubject () const   SConstScopedObject &  CNGAlignPanel::SetSubject ()   const TConstScopedObjects &  CNGAlignPanel::GetQueries () const   TConstScopedObjects &  CNGAlignPanel::SetQueries ()   wxBitmap  CNGAlignPanel::GetBitmapResource (const wxString &name)   wxIcon  CNGAlignPanel::GetIconResource (const wxString &name)   void  CNGAlignPanel::SetObjects (TConstScopedObjects *objects)   static bool  CNGAlignPanel::ShowToolTips ()     CPslLoadManager::CPslLoadManager ()   CPslLoadManager. More...
  static string  CPslLoadManager::Id ()   static string  CPslLoadManager::Label ()     CPslLoadManager::CPage::CPage (CPslLoadManager &manager)   virtual wxPanel *  CPslLoadManager::CPage::GetPanel ()   virtual bool  CPslLoadManager::CPage::CanLeavePage (bool)   CPslParamsPanel *  CPslLoadManager::x_GetParamsPanel ()     CTaxTreeToolPanel::CTaxTreeToolPanel ()     CTaxTreeToolPanel::CTaxTreeToolPanel (wxWindow *parent, wxWindowID id=ID_CTAXTREETOOLPANEL, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(400, 300), long style=wxTAB_TRAVERSAL, bool visibale=true)   bool  CTaxTreeToolPanel::Create (wxWindow *parent, wxWindowID id=ID_CTAXTREETOOLPANEL, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(400, 300), long style=wxTAB_TRAVERSAL, bool visibale=true)     CTaxTreeToolPanel::~CTaxTreeToolPanel ()   void  CTaxTreeToolPanel::Init ()   void  CTaxTreeToolPanel::CreateControls ()   virtual bool  CTaxTreeToolPanel::TransferDataFromWindow ()   CTaxTreeToolParams &  CTaxTreeToolPanel::GetData ()   const CTaxTreeToolParams &  CTaxTreeToolPanel::GetData () const   void  CTaxTreeToolPanel::SetData (const CTaxTreeToolParams &data)   wxBitmap  CTaxTreeToolPanel::GetBitmapResource (const wxString &name)   wxIcon  CTaxTreeToolPanel::GetIconResource (const wxString &name)   void  CTaxTreeToolPanel::SetObjects (map< string, TConstScopedObjects > *objects)   static bool  CTaxTreeToolPanel::ShowToolTips ()     CTextAlignLoaderManager::CTextAlignLoaderManager ()   CTextAlignLoaderManager. More...
  static string  CTextAlignLoaderManager::Id ()   static string  CTextAlignLoaderManager::Label ()     CTextAlignLoaderManager::CPage::CPage (CTextAlignLoaderManager &manager)   virtual wxPanel *  CTextAlignLoaderManager::CPage::GetPanel ()   virtual bool  CTextAlignLoaderManager::CPage::CanLeavePage (bool)   CTextAlignParamsPanel *  CTextAlignLoaderManager::x_GetParamsPanel ()   ◆ NET_BLAST_DM_TOOL_NAME ◆ NET_BLAST_LOADER_LABEL ◆ TAlignVector [1/2] ◆ TAlignVector [2/2] ◆ TAnnotVector ◆ TDbMap ◆ TDescriptors [1/4] ◆ TDescriptors [2/4] ◆ TDescriptors [3/4] ◆ TDescriptors [4/4] ◆ TGeneCDSmRNAList

a loader might be tied with a specific project item.

if so, we need to know such that they will go together and get added to the same project.

Definition at line 130 of file create_gene_model_tool_manager.hpp.

◆ TGeneModelMap ◆ TIdMap ◆ TItemDeque ◆ TItemRef ◆ TJobDescrVec ◆ TLoaderRef ◆ TLocPair ◆ TMRUDatabases ◆ TMRUQueries ◆ TNameToItemMap ◆ TObjects [1/8] ◆ TObjects [2/8] ◆ TObjects [3/8] ◆ TObjects [4/8] ◆ TObjects [5/8] ◆ TObjects [6/8] ◆ TObjects [7/8] ◆ TObjects [8/8] ◆ TPair ◆ TProgramAttrMap ◆ TProgramParamsMap ◆ TRepeatLibs ◆ TSeqTypeMap ◆ TStates ◆ TTaxIdLabelMap ◆ TUserFields ◆ TViews ◆ anonymous enum Enumerator ID_CMUSCLEPANEL  ID_PANEL  ID_CHOICE2  ID_CHECKBOX12  ID_TEXTCTRL11  ID_TEXTCTRL12  ID_BITMAPBUTTON1 

Definition at line 130 of file muscle_tool_panel.hpp.

◆ anonymous enum Enumerator ID_CNGALIGNPANEL  ID_QUERY_LIST  ID_SUBJ_LIST 

Definition at line 125 of file ngalign_panel.hpp.

◆ anonymous enum ◆ anonymous enum Enumerator ID_CBLAST_DB_DIALOG  ID_SEARCH  ID_RESET_BTN  wxID_STATUS  ID_TREECTRL 

Definition at line 173 of file blast_db_dialog.hpp.

◆ anonymous enum Enumerator ID_CBLASTSEARCHOPTIONSPANEL  ID_NUC_RADIO  ID_PROT_RADIO  ID_QUERY_SEQ_SET  ID_LIST  ID_PROGRAM_COMBO  ID_RADIOBUTTON  ID_RADIOBUTTON2  ID_RADIOBUTTON1  ID_SUBJECT_SEQ_SET  ID_SUBJ_LIST  ID_DB_COMBO  ID_SELECT_NCBI_DB  ID_ENTREZ_COMBO  ID_TEXTCTRL  ID_SELECT_LOCAL_DB_BTN  ID_CHECKBOX 

Definition at line 165 of file blast_search_options_panel.hpp.

◆ anonymous enum ◆ anonymous enum Enumerator ID_CBLASTSEARCHPARAMSPANEL  ID_WORDSIZE  ID_E_VALUE  ID_THRESHOLD  ID_GEN_CODE  ID_COMBOBOX  ID_LOW_COMPLEXITY  ID_STATIC_REPEAT_TYPE  ID_REPEAT_TYPE  ID_MASK_LOWERCASE  ID_MASK_REPEATS  ID_WMTI_CHOICE  ID_BUTTON  ID_ADV_TEXT  ID_COMPARTMENTS  ID_TITLE_TEXT  ID_STANDALONE 

Definition at line 197 of file blast_search_params_panel.hpp.

◆ anonymous enum ◆ anonymous enum Enumerator ID_CCLEANUPALIGNMENTSPARAMSPANEL  ID_LISTCTRL2  ID_COMBOBOX  ID_TEXTCTRL1  ID_TEXTCTRL  ID_CHECKBOX1  ID_CHECKBOX2  ID_CHECKBOX  ID_CHECKBOX5 

Definition at line 181 of file cleanup_alignments_params_panel.hpp.

◆ anonymous enum Enumerator ID_CFINDOVERLAPPANEL  ID_LISTCTRL3  ID_LISTCTRL4  ID_TEXTCTRL2  ID_TEXTCTRL4  ID_TEXTCTRL5 

Definition at line 124 of file find_overlap_panel.hpp.

◆ anonymous enum Enumerator ID_CGROUPALIGNMENTSPARAMSPANEL  ID_LISTCTRL  ID_CHECKBOX_SEQID  ID_CHECKBOX_STRAND  ID_CHECKBOX_TAXID  ID_CHECKBOX_SIMILAR_TAXID  ID_CHECKBOX_REFSEQ  ID_CHECKBOX_EST  ID_CHECKBOX_REFSEQ_PREDICTED  ID_CHECKBOX_GENBANK  ID_CHECKBOX_WGS  ID_CHECKBOX_HTGS  ID_CHECKBOX_PATENT 

Definition at line 165 of file group_alignments_params_panel.hpp.

◆ anonymous enum Enumerator ID_CBLASTSEARCHOPTIONSPANEL  ID_LISTCTRL1  ID_CHECKBOX6  ID_CHECKBOX7  ID_CHECKBOX8  ID_CHECKBOX9  ID_CHECKBOX10 

Definition at line 149 of file merge_alignments_params_panel.hpp.

◆ anonymous enum Enumerator ID_CNETBLASTDMSEARCHFORM  ID_FILTER_INPUT  ID_SUBMITTED_CHECK  ID_COMPLETED_CHECK  ID_FAILED_CHECK  ID_RETRIEVED_CHECK  ID_EXPIRED_CHECK 

Definition at line 139 of file net_blast_dm_search_form_panel.hpp.

◆ anonymous enum ◆ anonymous enum ◆ anonymous enum Enumerator ID_CSPLIGNPANEL  ID_PANEL1  ID_PANEL2  ID_CHOICE3  ID_CHOICE4  ID_CHECKBOX3  ID_CHECKBOX4  ID_TEXTCTRL7  ID_TEXTCTRL6  ID_TEXTCTRL8  ID_TEXTCTRL9  ID_TEXTCTRL13 

Definition at line 159 of file splign_panel.hpp.

◆ anonymous enum Enumerator ID_CTreeBuilderPanel  ID_LISTCTRL3  ID_LISTCTRL4  ID_TEXTCTRL2  ID_TEXTCTRL3  ID_TEXTCTRL4  ID_TEXTCTRL5 

Definition at line 126 of file tree_builder_panel.hpp.

◆ EAlgorithm ◆ ECommand Enumerator eInvalid  eSubmit  eMonitor 

submit request, monitor and retrieve results

eRetrieve 

monitor and retrieve resutlts

eFinished 

only retrieve resutlts

Definition at line 84 of file blast_search_task.hpp.

◆ EEventId ◆ EFreeEndType ◆ ENetBlastCommands

commands introduced by Net BLAST data source

Enumerator eCmdRetriveBlastJobs  eCmdMonitorBlastJobs  eCmdDeleteBlastJobs  eCmdExploreNetBLAST  eCmdLoadRIDs  eCmdBlastWinMask 

Definition at line 71 of file net_blast_ui_data_source.hpp.

◆ EState [1/5] ◆ EState [2/5] Enumerator eInvalidState  eInitial  eSubmitted  eCompleted  eFailed  eRetrieved  eExpired 

Definition at line 69 of file net_blast_job_descr.hpp.

◆ EState [3/5] ◆ EState [4/5] ◆ EState [5/5] ◆ ESubjectType ◆ MolType Enumerator kGenomic  kCDNA  kProtein  kNucleotide 

Definition at line 77 of file splign_panel.hpp.

◆ AddChild() ◆ AppliedEditToDataSource() void CPhyTreeView::AppliedEditToDataSource ( ) inline ◆ AttachClient() ◆ AutoCreateDefaultDataSource() bool CNetBLASTUIDataSourceType::AutoCreateDefaultDataSource ( ) virtual ◆ BeforeRun() bool CMSAToolJob::BeforeRun ( ) protectedvirtual

Function will be called on the main thread before execution of Run Should not do any lengthy work returns true to continue job execution on worker thread false to quit execution with status - failed.

Reimplemented from IAppJob.

Definition at line 158 of file msa_tool_job.cpp.

References env, eUnknown, GUI_AsyncExec(), Info(), ITERATE, LOG_POST, CMSAToolJob::m_CmdLine, CMSAToolJob::m_IdMap, CMSAToolJob::m_PId, CMSAToolJob::m_Ranges, CMSAToolJob::m_SeqTypes, CMSAToolJob::m_TmpIn, CMSAToolJob::m_TmpOut, CMSAToolJob::m_ToolName, NCBI_THROW, s_DumpSequences_wRange(), wxT, CMSAToolJob::x_GetCommandLine(), CMSAToolJob::x_GetObjects(), and CMSAToolJob::x_GetWorkingDirectory().

◆ BroadcastVisibleRange() ◆ CAdvancedCleanupTool() CAdvancedCleanupTool::CAdvancedCleanupTool ( ) ◆ CAlignSpanView() ◆ CanDo() [1/4] ◆ CanDo() [2/4] ◆ CanDo() [3/4] ◆ CanDo() [4/4] ◆ CanDoNext() bool CBLASTSearchOptionsPanel::CanDoNext ( ) ◆ CanGuessFormat() virtual bool CTextAlignLoaderManager::CanGuessFormat ( ) const inlinevirtual ◆ CanLeavePage() [1/2] virtual bool CPslLoadManager::CPage::CanLeavePage ( bool  ) inlinevirtual ◆ CanLeavePage() [2/2] virtual bool CTextAlignLoaderManager::CPage::CanLeavePage ( bool  ) inlinevirtual ◆ CAnnotCompareView() ◆ CanQuickLaunch() [1/5] bool CBLASTToolManager::CanQuickLaunch ( ) const virtual ◆ CanQuickLaunch() [2/5] virtual bool CKalignTool::CanQuickLaunch ( ) const inlineprotectedvirtual ◆ CanQuickLaunch() [3/5] virtual bool CMafftTool::CanQuickLaunch ( ) const inlineprotectedvirtual ◆ CanQuickLaunch() [4/5] virtual bool CMuscleTool::CanQuickLaunch ( ) const inlineprotectedvirtual ◆ CanQuickLaunch() [5/5] virtual bool CSplignTool::CanQuickLaunch ( ) const inlineprotectedvirtual ◆ CBLAST_DB_Dialog() [1/2] CBLAST_DB_Dialog::CBLAST_DB_Dialog ( ) ◆ CBLAST_DB_Dialog() [2/2] CBLAST_DB_Dialog::CBLAST_DB_Dialog ( wxWindow *  parent, wxWindowID  id = ID_CBLAST_DB_DIALOG, const wxString &  caption = wxEmptyString, const wxPoint &  pos = wxDefaultPosition, const wxSize &  size = wxSize(400, 300), long  style = wxCAPTION|wxRESIZE_BORDER|wxSYSTEM_MENU|wxCLOSE_BOX|wxTAB_TRAVERSAL  ) ◆ CBLAST_Dlg_Item() [1/2] ◆ CBLAST_Dlg_Item() [2/2] ◆ CBLASTParams() CBLASTParams::CBLASTParams ( )

Definition at line 248 of file blast_search_params.cpp.

References eBlastn, eBlastp, eBlastx, eDiscMegablast, eMegablast, map_checker< Container >::empty(), eTblastn, eTblastx, i, info, map_checker< Container >::insert(), CBLASTParams::m_ProgToParams, n, s_DefaultParams(), sc_ProgPairs, and CBLASTParams::sm_ProgramToAttr.

◆ CBLASTSearchOptionsPanel() [1/2] CBLASTSearchOptionsPanel::CBLASTSearchOptionsPanel ( ) ◆ CBLASTSearchOptionsPanel() [2/2] CBLASTSearchOptionsPanel::CBLASTSearchOptionsPanel ( wxWindow *  parent, wxWindowID  id = ID_CBLASTSEARCHOPTIONSPANEL, const wxPoint &  pos = wxDefaultPosition, const wxSize &  size = wxSize(), long  style = wxTAB_TRAVERSAL  ) ◆ CBLASTSearchParamsPanel() [1/2] CBLASTSearchParamsPanel::CBLASTSearchParamsPanel ( ) ◆ CBLASTSearchParamsPanel() [2/2] CBLASTSearchParamsPanel::CBLASTSearchParamsPanel ( wxWindow *  parent, wxWindowID  id = ID_CBLASTSEARCHPARAMSPANEL, const wxPoint &  pos = wxDefaultPosition, const wxSize &  size = wxSize(), long  style = wxTAB_TRAVERSAL  ) ◆ CBlastSearchTask() ◆ CBLASTSeqToolJob() ◆ CBLASTToolManager() CBLASTToolManager::CBLASTToolManager ( ) ◆ CCleanupAlignmentsJob() ◆ CCleanupAlignmentsParamsPanel() [1/2] CCleanupAlignmentsParamsPanel::CCleanupAlignmentsParamsPanel ( ) ◆ CCleanupAlignmentsParamsPanel() [2/2] CCleanupAlignmentsParamsPanel::CCleanupAlignmentsParamsPanel ( wxWindow *  parent, wxWindowID  id = ID_CCLEANUPALIGNMENTSPARAMSPANEL, const wxPoint &  pos = wxDefaultPosition, const wxSize &  size = wxSize(400, 300), long  style = wxTAB_TRAVERSAL  ) ◆ CCleanupAlignmentsToolManager() ◆ CClustalOmegaTool() CClustalOmegaTool::CClustalOmegaTool ( ) ◆ CClustalOmegaToolJob() ◆ CClustalOmegaToolParams() [1/2] CClustalOmegaToolParams::CClustalOmegaToolParams ( ) ◆ CClustalOmegaToolParams() [2/2] ◆ CClustalwTool() CClustalwTool::CClustalwTool ( ) ◆ CClustalwToolJob() ◆ CClustalwToolParams() [1/2] CClustalwToolParams::CClustalwToolParams ( ) ◆ CClustalwToolParams() [2/2] ◆ CCommonTaxTreeTool() CCommonTaxTreeTool::CCommonTaxTreeTool ( ) ◆ CCreateGeneModelTask() ◆ CCreateGeneModelToolManager() ◆ CCreateNeedlemanWunschJob() ◆ CCreateNeedlemanWunschToolManager() ◆ CCrossAlignView() ◆ CDebugMacroToolJob() ◆ CDotMatrixView() ◆ CDotMatrixViewFactory() CDotMatrixViewFactory::CDotMatrixViewFactory ( ) ◆ CFindOverlapPanel() [1/2] CFindOverlapPanel::CFindOverlapPanel ( ) ◆ CFindOverlapPanel() [2/2] CFindOverlapPanel::CFindOverlapPanel ( wxWindow *  parent, wxWindowID  id = ID_CFINDOVERLAPPANEL, const wxPoint &  pos = wxDefaultPosition, const wxSize &  size = wxSize(400, 300), long  style = wxTAB_TRAVERSAL, bool  visible = true  ) ◆ CFindOverlapParams() [1/2] CFindOverlapParams::CFindOverlapParams ( ) ◆ CFindOverlapParams() [2/2] ◆ CFindOverlapTool() CFindOverlapTool::CFindOverlapTool ( ) ◆ CGroupAlignmentsJob() ◆ CGroupAlignmentsParamsPanel() [1/2] CGroupAlignmentsParamsPanel::CGroupAlignmentsParamsPanel ( ) ◆ CGroupAlignmentsParamsPanel() [2/2] CGroupAlignmentsParamsPanel::CGroupAlignmentsParamsPanel ( wxWindow *  parent, wxWindowID  id = ID_CGROUPALIGNMENTSPARAMSPANEL, const wxPoint &  pos = wxDefaultPosition, const wxSize &  size = wxSize(400, 300), long  style = wxTAB_TRAVERSAL  ) ◆ CGroupAlignmentsToolManager() ◆ Check() void CNetBlastJobDescriptor::Check ( )

Definition at line 303 of file net_blast_job_descr.cpp.

References done, CNetBlastJobDescriptor::eCompleted, CNetBlastJobDescriptor::eExpired, CNetBlastJobDescriptor::eFailed, CNetBlastJobDescriptor::eInitial, CNetBlastJobDescriptor::eSubmitted, eUnknown, CNetBlastJobDescriptor::m_Errors, CNetBlastJobDescriptor::m_Mutex, CNetBlastJobDescriptor::m_RemoteBlast, CNetBlastJobDescriptor::m_State, NCBI_THROW, CNetBlastJobDescriptor::x_CreateRemoteBlastIfNeeded(), and CNetBlastJobDescriptor::x_NotifyDataSource().

Referenced by CNetBlastLoadingJob::x_CreateProjectItems().

◆ CKalignTool() CKalignTool::CKalignTool ( ) ◆ CKalignToolJob() ◆ CKalignToolParams() [1/2] CKalignToolParams::CKalignToolParams ( ) ◆ CKalignToolParams() [2/2] ◆ CleanUI() [1/21] void CBLASTToolManager::CleanUI ( ) virtual ◆ CleanUI() [2/21] void CCleanupAlignmentsToolManager::CleanUI ( ) virtual ◆ CleanUI() [3/21] void CClustalOmegaTool::CleanUI ( ) virtual ◆ CleanUI() [4/21] void CClustalwTool::CleanUI ( ) virtual ◆ CleanUI() [5/21] void CCreateGeneModelToolManager::CleanUI ( ) virtual ◆ CleanUI() [6/21] void CFindOverlapTool::CleanUI ( ) virtual ◆ CleanUI() [7/21] void CGroupAlignmentsToolManager::CleanUI ( ) virtual ◆ CleanUI() [8/21] void CKalignTool::CleanUI ( ) virtual ◆ CleanUI() [9/21] void CMafftTool::CleanUI ( ) virtual ◆ CleanUI() [10/21] void CMergeAlignmentsToolManager::CleanUI ( ) virtual ◆ CleanUI() [11/21] void CMuscleTool::CleanUI ( ) virtual ◆ CleanUI() [12/21] void CNetBLASTUILoadManager::CleanUI ( ) virtual ◆ CleanUI() [13/21] void CNGAlignTool::CleanUI ( ) virtual ◆ CleanUI() [14/21] void CProSplignTool::CleanUI ( ) virtual ◆ CleanUI() [15/21] void CSplignTool::CleanUI ( ) virtual ◆ CleanUI() [16/21] void CCommonTaxTreeTool::CleanUI ( ) virtual ◆ CleanUI() [17/21] void CTreeBuilderTool::CleanUI ( ) virtual ◆ CleanUI() [18/21] void CAdvancedCleanupTool::CleanUI ( ) virtual ◆ CleanUI() [19/21] void CCreateNeedlemanWunschToolManager::CleanUI ( ) virtual ◆ CleanUI() [20/21] void CPslLoadManager::CleanUI ( ) virtual ◆ CleanUI() [21/21] void CTextAlignLoaderManager::CleanUI ( ) virtual ◆ Clone() IUITool * CNetBLAST_DMSearchTool::Clone ( void  ) const virtual ◆ Close() bool CNetBLASTUIDataSource::Close ( void  ) virtual

Implements IUIDataSource.

Definition at line 256 of file net_blast_ui_data_source.cpp.

References CStopWatch::AsSmartString(), ERR_POST, CStopWatch::eStart, CExtensionRegistry::GetInstance(), Info(), kAppExpCmdExtPoint, kCmdExtPoint, CNetBLASTUIDataSource::m_JobDescrs, CNetBLASTUIDataSource::m_Open, CStopWatch::Restart(), CStopWatch::Stop(), and CNetBLASTUIDataSource::x_SaveJobDescriptors().

◆ CMafftTool() CMafftTool::CMafftTool ( ) ◆ CMafftToolJob() ◆ CMafftToolParams() [1/2] CMafftToolParams::CMafftToolParams ( ) ◆ CMafftToolParams() [2/2] ◆ CMergeAlignmentsJob() ◆ CMergeAlignmentsParamsPanel() [1/2] CMergeAlignmentsParamsPanel::CMergeAlignmentsParamsPanel ( ) ◆ CMergeAlignmentsParamsPanel() [2/2] CMergeAlignmentsParamsPanel::CMergeAlignmentsParamsPanel ( wxWindow *  parent, wxWindowID  id = ID_CBLASTSEARCHOPTIONSPANEL, const wxPoint &  pos = wxDefaultPosition, const wxSize &  size = wxSize(400, 300), long  style = wxTAB_TRAVERSAL  ) ◆ CMergeAlignmentsToolManager() CMergeAlignmentsToolManager::CMergeAlignmentsToolManager ( ) ◆ CMolTypeValidator() ◆ CMPCrossAlignView() ◆ CMSAToolJob() CMSAToolJob::CMSAToolJob ( const wxString &  tool_name ) ◆ CMultiAlignView() CMultiAlignView::CMultiAlignView ( ) ◆ CMultiAlignViewFactory() CMultiAlignViewFactory::CMultiAlignViewFactory ( ) ◆ CMuscleTool() CMuscleTool::CMuscleTool ( ) ◆ CMuscleToolJob() ◆ CMuscleToolPanel() [1/2] CMuscleToolPanel::CMuscleToolPanel ( ) ◆ CMuscleToolPanel() [2/2] CMuscleToolPanel::CMuscleToolPanel ( wxWindow *  parent, wxWindowID  id = ID_CMUSCLEPANEL, const wxPoint &  pos = wxDefaultPosition, const wxSize &  size = wxSize(400, 300), long  style = wxTAB_TRAVERSAL, bool  visible = true  ) ◆ CMuscleToolParams() [1/2] CMuscleToolParams::CMuscleToolParams ( ) ◆ CMuscleToolParams() [2/2] ◆ CNeedlemanWunschToolParams() [1/2] CNeedlemanWunschToolParams::CNeedlemanWunschToolParams ( ) ◆ CNeedlemanWunschToolParams() [2/2] ◆ CNetBLAST_DMSearchForm() ◆ CNetBLAST_DMSearchJob() ◆ CNetBLAST_DMSearchQuery() ◆ CNetBLAST_DMSearchTool() CNetBLAST_DMSearchTool::CNetBLAST_DMSearchTool ( ) ◆ CNetBlastDMSearchFormPanel() [1/2] CNetBlastDMSearchFormPanel::CNetBlastDMSearchFormPanel ( ) ◆ CNetBlastDMSearchFormPanel() [2/2] CNetBlastDMSearchFormPanel::CNetBlastDMSearchFormPanel ( wxWindow *  parent, wxWindowID  id = ID_CNETBLASTDMSEARCHFORM, const wxPoint &  pos = wxDefaultPosition, const wxSize &  size = wxDefaultSize, long  style = wxTAB_TRAVERSAL  ) ◆ CNetBlastJobDescriptor() [1/3] CNetBlastJobDescriptor::CNetBlastJobDescriptor ( ) protected ◆ CNetBlastJobDescriptor() [2/3] ◆ CNetBlastJobDescriptor() [3/3] ◆ CNetBlastLoadingJob() ◆ CNetBLASTLoadOptionPanel() [1/2] CNetBLASTLoadOptionPanel::CNetBLASTLoadOptionPanel ( ) ◆ CNetBLASTLoadOptionPanel() [2/2] CNetBLASTLoadOptionPanel::CNetBLASTLoadOptionPanel ( wxWindow *  parent, wxWindowID  id = ID_NETBLASTLOADOPTIONPANEL, const wxPoint &  pos = wxDefaultPosition, const wxSize &  size = wxSize(400, 300), long  style = wxTAB_TRAVERSAL  ) ◆ CNetBlastMonitoringJob() ◆ CNetBlastSubmittingJob() ◆ CNetBLASTUIDataSource() ◆ CNetBLASTUIDataSourceEvent() ◆ CNetBLASTUIDataSourceType() CNetBLASTUIDataSourceType::CNetBLASTUIDataSourceType ( ) ◆ CNetBLASTUILoadManager() ◆ CNGAlignJob() ◆ CNGAlignPanel() [1/2] CNGAlignPanel::CNGAlignPanel ( ) ◆ CNGAlignPanel() [2/2] CNGAlignPanel::CNGAlignPanel ( wxWindow *  parent ) ◆ CNGAlignParams() [1/2] CNGAlignParams::CNGAlignParams ( ) ◆ CNGAlignParams() [2/2] ◆ CNGAlignTool() CNGAlignTool::CNGAlignTool ( ) ◆ CombineInputObjects() ◆ CommitTheChanges() ◆ ConstructQuery()

Reimplemented from CSearchFormBase.

Definition at line 325 of file net_blast_dm_search_tool.cpp.

References CNetBlastJobDescriptor::eCompleted, CNetBlastJobDescriptor::eExpired, CNetBlastJobDescriptor::eFailed, CNetBlastJobDescriptor::eRetrieved, CNetBlastJobDescriptor::eSubmitted, CNetBlastDMSearchFormPanel::GetCompleted(), CNetBlastDMSearchFormPanel::GetExpired(), CNetBlastDMSearchFormPanel::GetFailed(), CNetBlastDMSearchFormPanel::GetRetrieved(), CNetBlastDMSearchFormPanel::GetSearchValue(), CNetBlastDMSearchFormPanel::GetSubmitted(), set< Key, Compare >::insert(), CNetBLAST_DMSearchForm::m_Panel, CRef< C, Locker >::Reset(), and ToStdString().

◆ Copy() [1/11] ◆ Copy() [2/11] ◆ Copy() [3/11] ◆ Copy() [4/11] ◆ Copy() [5/11] ◆ Copy() [6/11] ◆ Copy() [7/11] ◆ Copy() [8/11]

Definition at line 79 of file ngalign_params.cpp.

References data, CNGAlignParams::m_AdvParams, CNGAlignParams::m_BestHit, CNGAlignParams::m_eValue, CNGAlignParams::m_FilterMode, CNGAlignParams::m_JobTitle, CNGAlignParams::m_Queries, CNGAlignParams::m_Subject, CNGAlignParams::m_WM_Dir, CNGAlignParams::m_WM_TaxId, and CNGAlignParams::m_WordSize.

Referenced by CNGAlignParams::CNGAlignParams(), and CNGAlignParams::operator=().

◆ Copy() [9/11]

Definition at line 71 of file splign_params.cpp.

References data, CSplignParams::m_cDNA_strand, CSplignParams::m_CompPenalty, CSplignParams::m_DiscType, CSplignParams::m_EndGapDetect, CSplignParams::m_MaxGenomicExtent, CSplignParams::m_MaxIntron, CSplignParams::m_MinCompIdentity, CSplignParams::m_MinExonIdentity, and CSplignParams::m_PolyADetect.

Referenced by CSplignParams::CSplignParams(), and CSplignParams::operator=().

◆ Copy() [10/11] ◆ Copy() [11/11] ◆ CPage() [1/2] ◆ CPage() [2/2] ◆ CPhyloTreeJob() CPhyloTreeJob::CPhyloTreeJob ( const objects::CBioTreeContainer *  btc ) ◆ CPhyTreeView() CPhyTreeView::CPhyTreeView ( ) ◆ CProSplignTool() CProSplignTool::CProSplignTool ( ) ◆ CPslLoadManager() CPslLoadManager::CPslLoadManager ( ) ◆ Create() [1/15] void CNetBLAST_DMSearchForm::Create ( void  ) virtual ◆ Create() [2/15] bool CBLAST_DB_Dialog::Create ( wxWindow *  parent, wxWindowID  id = ID_CBLAST_DB_DIALOG, const wxString &  caption = wxEmptyString, const wxPoint &  pos = wxDefaultPosition, const wxSize &  size = wxSize(400, 300), long  style = wxCAPTION|wxRESIZE_BORDER|wxSYSTEM_MENU|wxCLOSE_BOX|wxTAB_TRAVERSAL  ) ◆ Create() [3/15] bool CBLASTSearchOptionsPanel::Create ( wxWindow *  parent, wxWindowID  id = ID_CBLASTSEARCHOPTIONSPANEL, const wxPoint &  pos = wxDefaultPosition, const wxSize &  size = wxSize(), long  style = wxTAB_TRAVERSAL  ) ◆ Create() [4/15] bool CMergeAlignmentsParamsPanel::Create ( wxWindow *  parent, wxWindowID  id = ID_CBLASTSEARCHOPTIONSPANEL, const wxPoint &  pos = wxDefaultPosition, const wxSize &  size = wxSize(400, 300), long  style = wxTAB_TRAVERSAL  ) ◆ Create() [5/15] bool CBLASTSearchParamsPanel::Create ( wxWindow *  parent, wxWindowID  id = ID_CBLASTSEARCHPARAMSPANEL, const wxPoint &  pos = wxDefaultPosition, const wxSize &  size = wxSize(), long  style = wxTAB_TRAVERSAL  ) ◆ Create() [6/15] ◆ Create() [7/15] bool CFindOverlapPanel::Create ( wxWindow *  parent, wxWindowID  id = ID_CFINDOVERLAPPANEL, const wxPoint &  pos = wxDefaultPosition, const wxSize &  size = wxSize(400, 300), long  style = wxTAB_TRAVERSAL, bool  visible = true  ) ◆ Create() [8/15] bool CGroupAlignmentsParamsPanel::Create ( wxWindow *  parent, wxWindowID  id = ID_CGROUPALIGNMENTSPARAMSPANEL, const wxPoint &  pos = wxDefaultPosition, const wxSize &  size = wxSize(400, 300), long  style = wxTAB_TRAVERSAL  ) ◆ Create() [9/15] bool CMuscleToolPanel::Create ( wxWindow *  parent, wxWindowID  id = ID_CMUSCLEPANEL, const wxPoint &  pos = wxDefaultPosition, const wxSize &  size = wxSize(400, 300), long  style = wxTAB_TRAVERSAL, bool  visible = true  ) ◆ Create() [10/15] bool CNetBlastDMSearchFormPanel::Create ( wxWindow *  parent, wxWindowID  id = ID_CNETBLASTDMSEARCHFORM, const wxPoint &  pos = wxDefaultPosition, const wxSize &  size = wxDefaultSize, long  style = wxTAB_TRAVERSAL  ) ◆ Create() [11/15] ◆ Create() [12/15] bool CSplignPanel::Create ( wxWindow *  parent, wxWindowID  id = ID_CSPLIGNPANEL, const wxPoint &  pos = wxDefaultPosition, const wxSize &  size = wxSize(400, 300), long  style = wxCLIP_CHILDREN|wxTAB_TRAVERSAL, bool  visibale = true  ) ◆ Create() [13/15] bool CTaxTreeToolPanel::Create ( wxWindow *  parent, wxWindowID  id = ID_CTAXTREETOOLPANEL, const wxPoint &  pos = wxDefaultPosition, const wxSize &  size = wxSize(400, 300), long  style = wxTAB_TRAVERSAL, bool  visibale = true  ) ◆ Create() [14/15] bool CTreeBuilderPanel::Create ( wxWindow *  parent, wxWindowID  id = ID_CTreeBuilderPanel, const wxPoint &  pos = wxDefaultPosition, const wxSize &  size = wxSize(400, 300), long  style = wxTAB_TRAVERSAL  ) ◆ Create() [15/15] bool CNetBLASTLoadOptionPanel::Create ( wxWindow *  parent, wxWindowID  id = ID_NETBLASTLOADOPTIONPANEL, const wxPoint &  pos = wxDefaultPosition, const wxSize &  size = wxSize(400, 300), long  style = wxTAB_TRAVERSAL  ) ◆ CreateControls() [1/14] void CBLAST_DB_Dialog::CreateControls ( ) ◆ CreateControls() [2/14] void CBLASTSearchOptionsPanel::CreateControls ( )

Definition at line 205 of file blast_search_options_panel.cpp.

References _, CBLASTSearchOptionsPanel::GetBitmapResource(), CBLASTSearchOptionsPanel::ID_CHECKBOX, CBLASTSearchOptionsPanel::ID_DB_COMBO, CBLASTSearchOptionsPanel::ID_DBS_FAILED, CBLASTSearchOptionsPanel::ID_DBS_LOADING_PROGRESS, CBLASTSearchOptionsPanel::ID_DBS_LOADING_TEXT, CBLASTSearchOptionsPanel::ID_DBS_TRY_AGAIN, CBLASTSearchOptionsPanel::ID_ENTREZ_COMBO, CBLASTSearchOptionsPanel::ID_LIST, CBLASTSearchOptionsPanel::ID_NUC_RADIO, CBLASTSearchOptionsPanel::ID_PROGRAM_COMBO, CBLASTSearchOptionsPanel::ID_PROT_RADIO, CBLASTSearchOptionsPanel::ID_QUERY_SEQ_SET, CBLASTSearchOptionsPanel::ID_RADIOBUTTON, CBLASTSearchOptionsPanel::ID_RADIOBUTTON1, CBLASTSearchOptionsPanel::ID_RADIOBUTTON2, CBLASTSearchOptionsPanel::ID_SELECT_LOCAL_DB_BTN, CBLASTSearchOptionsPanel::ID_SELECT_NCBI_DB, CBLASTSearchOptionsPanel::ID_SUBJ_LIST, CBLASTSearchOptionsPanel::ID_SUBJECT_SEQ_SET, CBLASTSearchOptionsPanel::ID_TEXTCTRL, CBLASTSearchOptionsPanel::m_BrowseDBBtn, CBLASTSearchOptionsPanel::m_DatabaseCombo, CBLASTSearchOptionsPanel::m_DBSizer, CBLASTSearchOptionsPanel::m_LocalDBCtrl, CBLASTSearchOptionsPanel::m_LocalDBLoaderCtrl, CBLASTSearchOptionsPanel::m_LocalDBSizer, CBLASTSearchOptionsPanel::m_LocalSeqsSizer, CBLASTSearchOptionsPanel::m_LocalSizer, CBLASTSearchOptionsPanel::m_NCBIDBSizer, CBLASTSearchOptionsPanel::m_NucRadio, CBLASTSearchOptionsPanel::m_ProgramCombo, CBLASTSearchOptionsPanel::m_ProtRadio, CBLASTSearchOptionsPanel::m_QueryCombo, CBLASTSearchOptionsPanel::m_QueryListCtrl, CBLASTSearchOptionsPanel::m_QuerySeqSetCombo, CBLASTSearchOptionsPanel::m_QuerySeqSetStatic, CBLASTSearchOptionsPanel::m_SubjectListCtrl, CBLASTSearchOptionsPanel::m_SubjectSeqSetCombo, CBLASTSearchOptionsPanel::m_SubjectSeqSetStatic, CBLASTSearchOptionsPanel::m_SubjectTypeLDBCtrl, CBLASTSearchOptionsPanel::m_SubjectTypeNCBICtrl, CBLASTSearchOptionsPanel::m_SubjectTypeSeqsCtrl, CBLASTSearchOptionsPanel::ShowToolTips(), wxID_ANY, and wxT.

Referenced by CBLASTSearchOptionsPanel::Create().

◆ CreateControls() [3/14] void CBLASTSearchParamsPanel::CreateControls ( )

Definition at line 151 of file blast_search_params_panel.cpp.

References _, CBLASTParams::GetAllRepeatLibs(), CBLASTSearchParamsPanel::ID_ADV_TEXT, CBLASTSearchParamsPanel::ID_BUTTON, CBLASTSearchParamsPanel::ID_COMBOBOX, CBLASTSearchParamsPanel::ID_COMPARTMENTS, CBLASTSearchParamsPanel::ID_E_VALUE, CBLASTSearchParamsPanel::ID_GEN_CODE, CBLASTSearchParamsPanel::ID_LOADING_PROGRESS, CBLASTSearchParamsPanel::ID_LOADING_TEXT, CBLASTSearchParamsPanel::ID_LOW_COMPLEXITY, CBLASTSearchParamsPanel::ID_MASK_LOWERCASE, CBLASTSearchParamsPanel::ID_MASK_REPEATS, CBLASTSearchParamsPanel::ID_REPEAT_TYPE, CBLASTSearchParamsPanel::ID_STANDALONE, CBLASTSearchParamsPanel::ID_STATIC_REPEAT_TYPE, CBLASTSearchParamsPanel::ID_THRESHOLD, CBLASTSearchParamsPanel::ID_TITLE_TEXT, CBLASTSearchParamsPanel::ID_WMTI_CHOICE, CBLASTSearchParamsPanel::ID_WORDSIZE, ITERATE, CBLASTSearchParamsPanel::m_AdvParams, CBLASTSearchParamsPanel::m_chbStandalone, CBLASTSearchParamsPanel::m_CompartCheck, CBLASTSearchParamsPanel::m_DbGenCodeCombo, CBLASTSearchParamsPanel::m_DbGenCodeLabel, CBLASTSearchParamsPanel::m_DbGeneticCode, CBLASTSearchParamsPanel::m_eValue, CBLASTSearchParamsPanel::m_FilterLowComplex, CBLASTSearchParamsPanel::m_GeneralSizer, CBLASTSearchParamsPanel::m_JobTitle, CBLASTSearchParamsPanel::m_LCRegionsCheck, CBLASTSearchParamsPanel::m_MaskLCRegions, CBLASTSearchParamsPanel::m_MaskRepeats, CBLASTSearchParamsPanel::m_QueryGenCodeCombo, CBLASTSearchParamsPanel::m_QueryGenCodeLabel, CBLASTSearchParamsPanel::m_QueryGeneticCode, CBLASTSearchParamsPanel::m_RepeatsCheck, CBLASTSearchParamsPanel::m_RepeatType, CBLASTSearchParamsPanel::m_ThreshInput, CBLASTSearchParamsPanel::m_ThreshLabel, CBLASTSearchParamsPanel::m_Threshold, CBLASTSearchParamsPanel::m_WMDownload, CBLASTSearchParamsPanel::m_WMStatic, CBLASTSearchParamsPanel::m_WMStaticBoxSizer, CBLASTSearchParamsPanel::m_WMTaxIds, CBLASTSearchParamsPanel::m_WordSize, CBLASTSearchParamsPanel::ShowToolTips(), ToWxString(), wxID_ANY, wxT, and CBLASTSearchParamsPanel::x_InitGeneticCodesCombo().

Referenced by CBLASTSearchParamsPanel::Create().

◆ CreateControls() [4/14] void CCleanupAlignmentsParamsPanel::CreateControls ( )

Definition at line 144 of file cleanup_alignments_params_panel.cpp.

References _, CCleanupAlignmentsParamsPanel::ID_CHECKBOX, CCleanupAlignmentsParamsPanel::ID_CHECKBOX1, CCleanupAlignmentsParamsPanel::ID_CHECKBOX2, CCleanupAlignmentsParamsPanel::ID_CHECKBOX5, CCleanupAlignmentsParamsPanel::ID_COMBOBOX, CCleanupAlignmentsParamsPanel::ID_LISTCTRL2, CCleanupAlignmentsParamsPanel::ID_TEXTCTRL, CCleanupAlignmentsParamsPanel::ID_TEXTCTRL1, CCleanupAlignmentsParamsPanel::m_AlgoSelector, CCleanupAlignmentsParamsPanel::m_AlnMgr_FillUnaligned, CCleanupAlignmentsParamsPanel::m_AlnMgr_PreserveRows, CCleanupAlignmentsParamsPanel::m_AlnMgr_Sort, CCleanupAlignmentsParamsPanel::m_AlnMgr_Transloc, CCleanupAlignmentsParamsPanel::m_HitFilter_MinIdentity, CCleanupAlignmentsParamsPanel::m_HitFilter_MinLength, CCleanupAlignmentsParamsPanel::m_ObjectList, CCleanupAlignmentsParamsPanel::m_ParamsPanel, and wxID_ANY.

Referenced by CCleanupAlignmentsParamsPanel::Create().

◆ CreateControls() [5/14] void CFindOverlapPanel::CreateControls ( ) ◆ CreateControls() [6/14] void CGroupAlignmentsParamsPanel::CreateControls ( )

Definition at line 196 of file group_alignments_params_panel.cpp.

References _, CGroupAlignmentsParamsPanel::ID_CHECKBOX_EST, CGroupAlignmentsParamsPanel::ID_CHECKBOX_GENBANK, CGroupAlignmentsParamsPanel::ID_CHECKBOX_HTGS, CGroupAlignmentsParamsPanel::ID_CHECKBOX_PATENT, CGroupAlignmentsParamsPanel::ID_CHECKBOX_REFSEQ, CGroupAlignmentsParamsPanel::ID_CHECKBOX_REFSEQ_PREDICTED, CGroupAlignmentsParamsPanel::ID_CHECKBOX_SEQID, CGroupAlignmentsParamsPanel::ID_CHECKBOX_SIMILAR_TAXID, CGroupAlignmentsParamsPanel::ID_CHECKBOX_STRAND, CGroupAlignmentsParamsPanel::ID_CHECKBOX_TAXID, CGroupAlignmentsParamsPanel::ID_CHECKBOX_WGS, CGroupAlignmentsParamsPanel::ID_LISTCTRL, CGroupAlignmentsParamsPanel::m_GroupByEST, CGroupAlignmentsParamsPanel::m_GroupByGenBank, CGroupAlignmentsParamsPanel::m_GroupByHTGS, CGroupAlignmentsParamsPanel::m_GroupByLikeTaxId, CGroupAlignmentsParamsPanel::m_GroupByPatent, CGroupAlignmentsParamsPanel::m_GroupByPredictedRefSeq, CGroupAlignmentsParamsPanel::m_GroupByRefSeq, CGroupAlignmentsParamsPanel::m_GroupBySeqId, CGroupAlignmentsParamsPanel::m_GroupByStrand, CGroupAlignmentsParamsPanel::m_GroupByTaxId, CGroupAlignmentsParamsPanel::m_GroupByWGS, CGroupAlignmentsParamsPanel::m_ObjectList, and wxID_ANY.

Referenced by CGroupAlignmentsParamsPanel::Create().

◆ CreateControls() [7/14] void CMergeAlignmentsParamsPanel::CreateControls ( )

Definition at line 169 of file merge_alignments_params_panel.cpp.

References _, CMergeAlignmentsParamsPanel::ID_CHECKBOX10, CMergeAlignmentsParamsPanel::ID_CHECKBOX6, CMergeAlignmentsParamsPanel::ID_CHECKBOX7, CMergeAlignmentsParamsPanel::ID_CHECKBOX8, CMergeAlignmentsParamsPanel::ID_CHECKBOX9, CMergeAlignmentsParamsPanel::ID_LISTCTRL1, CMergeAlignmentsParamsPanel::m_AssumeNegStrand, CMergeAlignmentsParamsPanel::m_FillUnaligned, CMergeAlignmentsParamsPanel::m_MergeQuerySeqOnly, CMergeAlignmentsParamsPanel::m_ObjectListCtrl, CMergeAlignmentsParamsPanel::m_SortInput, CMergeAlignmentsParamsPanel::m_TruncateOverlap, and wxID_ANY.

Referenced by CMergeAlignmentsParamsPanel::Create().

◆ CreateControls() [8/14] void CNetBlastDMSearchFormPanel::CreateControls ( )

Definition at line 121 of file net_blast_dm_search_form_panel.cpp.

References CNetBlastDMSearchFormPanel::ID_COMPLETED_CHECK, CNetBlastDMSearchFormPanel::ID_EXPIRED_CHECK, CNetBlastDMSearchFormPanel::ID_FAILED_CHECK, CNetBlastDMSearchFormPanel::ID_FILTER_INPUT, CNetBlastDMSearchFormPanel::ID_RETRIEVED_CHECK, CNetBlastDMSearchFormPanel::ID_SUBMITTED_CHECK, CNetBlastDMSearchFormPanel::m_Completed, CNetBlastDMSearchFormPanel::m_Expired, CNetBlastDMSearchFormPanel::m_Failed, CNetBlastDMSearchFormPanel::m_ResetBtn, CNetBlastDMSearchFormPanel::m_Retrieved, CNetBlastDMSearchFormPanel::m_SearchCtrl, CNetBlastDMSearchFormPanel::m_SearchValue, CNetBlastDMSearchFormPanel::m_Submitted, and wxT.

Referenced by CNetBlastDMSearchFormPanel::Create().

◆ CreateControls() [9/14] void CNetBLASTLoadOptionPanel::CreateControls ( ) ◆ CreateControls() [10/14] void CSplignPanel::CreateControls ( )

Definition at line 201 of file splign_panel.cpp.

References _, CSplignPanel::GetData(), CSplignPanel::ID_CHECKBOX3, CSplignPanel::ID_CHECKBOX4, CSplignPanel::ID_CHOICE3, CSplignPanel::ID_CHOICE4, CSplignPanel::ID_PANEL1, CSplignPanel::ID_PANEL2, CSplignPanel::ID_TEXTCTRL13, CSplignPanel::ID_TEXTCTRL6, CSplignPanel::ID_TEXTCTRL7, CSplignPanel::ID_TEXTCTRL8, CSplignPanel::ID_TEXTCTRL9, CSplignPanel::m_cDNAList, CSplignPanel::m_CDNAListAccValidator, CSplignPanel::m_GenomicList, CSplignPanel::m_GenomicListAccValidator, CObjectListWidgetSel::SetAccessionValidator(), CObjectListWidgetSel::SetDoSelectAll(), CObjectListWidgetSel::SetTitle(), and wxT.

Referenced by CSplignPanel::Create().

◆ CreateControls() [11/14] void CTreeBuilderPanel::CreateControls ( )

Definition at line 113 of file tree_builder_panel.cpp.

References _, CTreeBuilderPanel::ID_LISTCTRL3, CTreeBuilderPanel::ID_TEXTCTRL2, CTreeBuilderPanel::ID_TEXTCTRL3, CTreeBuilderPanel::ID_TEXTCTRL4, CTreeBuilderPanel::m_pConstruct, CTreeBuilderPanel::m_pDistance, CTreeBuilderPanel::m_pLabels, CTreeBuilderPanel::m_Seq1List, sc_FastMe(), sc_JukesCantor(), sc_Kimura(), sc_Nj(), sc_Poisson(), sc_SeqId(), sc_SeqTitle(), sc_TaxName(), ToWxString(), wxID_ANY, and wxT.

Referenced by CTreeBuilderPanel::Create().

◆ CreateControls() [12/14] void CMuscleToolPanel::CreateControls ( )

Definition at line 113 of file muscle_tool_panel.cpp.

References _, CObjectListWidgetSel::EnableGroups(), CMuscleToolPanel::GetBitmapResource(), CMuscleToolPanel::GetData(), CMuscleToolPanel::ID_BITMAPBUTTON1, CMuscleToolPanel::ID_CHECKBOX12, CMuscleToolPanel::ID_CHOICE2, CMuscleToolPanel::ID_PANEL, CMuscleToolPanel::ID_TEXTCTRL11, CMuscleToolPanel::ID_TEXTCTRL12, CMuscleToolPanel::m_LocationSel, CObjectListWidgetSel::SetDefaultSelection(), CObjectListWidgetSel::SetDoSelectAll(), CObjectListWidgetSel::SetTitle(), CObjectListWidgetSel::ShowNuclProtButtons(), CMuscleToolPanel::ShowToolTips(), and wxT.

Referenced by CMuscleToolPanel::Create().

◆ CreateControls() [13/14] void CNGAlignPanel::CreateControls ( ) ◆ CreateControls() [14/14] void CTaxTreeToolPanel::CreateControls ( ) ◆ CreateDataSource() ◆ CreateEvtHandler() wxEvtHandler * CNetBLASTUIDataSource::CreateEvtHandler ( ) virtual ◆ CreateInstance() [1/7] IView * CAlignSpanViewFactory::CreateInstance ( ) const virtual ◆ CreateInstance() [2/7] IView * CAnnotCompareViewFactory::CreateInstance ( ) const virtual ◆ CreateInstance() [3/7] IView * CCrossAlignViewFactory::CreateInstance ( ) const virtual ◆ CreateInstance() [4/7] IView * CDotMatrixViewFactory::CreateInstance ( ) const virtual ◆ CreateInstance() [5/7] IView * CMPCrossAlignViewFactory::CreateInstance ( ) const virtual ◆ CreateInstance() [6/7] IView * CMultiAlignViewFactory::CreateInstance ( ) const virtual ◆ CreateInstance() [7/7] IView * CPhyTreeViewFactory::CreateInstance ( ) const virtual ◆ CreateInstanceByFingerprint() [1/7] ◆ CreateInstanceByFingerprint() [2/7] ◆ CreateInstanceByFingerprint() [3/7] ◆ CreateInstanceByFingerprint() [4/7] ◆ CreateInstanceByFingerprint() [5/7] ◆ CreateInstanceByFingerprint() [6/7] ◆ CreateInstanceByFingerprint() [7/7] ◆ CreateJobDescriptor() [1/2] ◆ CreateJobDescriptor() [2/2] ◆ CreateSearchForm() ◆ CreateViewWindow() [1/7] void CAlignSpanView::CreateViewWindow ( wxWindow *  parent ) virtual ◆ CreateViewWindow() [2/7] void CAnnotCompareView::CreateViewWindow ( wxWindow *  parent ) virtual ◆ CreateViewWindow() [3/7] void CCrossAlignView::CreateViewWindow ( wxWindow *  parent ) virtual ◆ CreateViewWindow() [4/7] void CDotMatrixView::CreateViewWindow ( wxWindow *  parent ) virtual ◆ CreateViewWindow() [5/7] void CMPCrossAlignView::CreateViewWindow ( wxWindow *  parent ) virtual ◆ CreateViewWindow() [6/7] void CMultiAlignView::CreateViewWindow ( wxWindow *  parent ) virtual

create Window corresponding to the view

Implements CProjectViewBase.

Definition at line 162 of file multi_align_view.cpp.

References _ASSERT, CEventHandler::AddListener(), CAlnMultiWidget::CreateWidget(), CEventHandler::ePool_Child, CEventHandler::ePool_Parent, CAlnMultiWidget::GetDisplayStyle(), CMultiAlignView::m_AlnWidget, CMultiAlignView::m_StyleCatalog, CRowStyleCatalog::SetDefaultStyle(), CAlnMultiWidget::SetStyleCatalog(), and CRowStyleCatalog::SetWidgetStyle().

◆ CreateViewWindow() [7/7] void CPhyTreeView::CreateViewWindow ( wxWindow *  parent ) virtual

create Window corresponding to the view

Implements CProjectViewBase.

Definition at line 793 of file phy_tree_view.cpp.

References _ASSERT, CEventHandler::AddListener(), CGlWidgetBase::Create(), CQueryParsePanel::Create(), CEventHandler::ePool_Child, CEventHandler::ePool_Parent, CRef< C, Locker >::GetPointerOrNull(), CPhyTreeView::kPhylpWidgetID, CPhyTreeView::kQueryPanelID, CPhyTreeView::m_DataSource, CPhyTreeView::m_Panel, and CPhyloTreeWidget::SetQueryPanel().

◆ CrossLinkTriple() void SGeneCdsmRnaFeats::CrossLinkTriple ( ) ◆ CSelRowHandle() ◆ CSplignPanel() [1/2] CSplignPanel::CSplignPanel ( ) ◆ CSplignPanel() [2/2] CSplignPanel::CSplignPanel ( wxWindow *  parent, wxWindowID  id = ID_CSPLIGNPANEL, const wxPoint &  pos = wxDefaultPosition, const wxSize &  size = wxSize(400, 300), long  style = wxCLIP_CHILDREN|wxTAB_TRAVERSAL, bool  visibale = true  ) ◆ CSplignParams() [1/2] CSplignParams::CSplignParams ( ) ◆ CSplignParams() [2/2] ◆ CSplignTool() CSplignTool::CSplignTool ( ) ◆ CTaxTreeToolJob() ◆ CTaxTreeToolPanel() [1/2] CTaxTreeToolPanel::CTaxTreeToolPanel ( ) ◆ CTaxTreeToolPanel() [2/2] CTaxTreeToolPanel::CTaxTreeToolPanel ( wxWindow *  parent, wxWindowID  id = ID_CTAXTREETOOLPANEL, const wxPoint &  pos = wxDefaultPosition, const wxSize &  size = wxSize(400, 300), long  style = wxTAB_TRAVERSAL, bool  visibale = true  ) ◆ CTaxTreeToolParams() [1/2] CTaxTreeToolParams::CTaxTreeToolParams ( ) ◆ CTaxTreeToolParams() [2/2] ◆ CTextAlignLoaderManager() CTextAlignLoaderManager::CTextAlignLoaderManager ( ) ◆ CTextAlignObjectLoader() [1/2] ◆ CTextAlignObjectLoader() [2/2] ◆ CTreeBuilderPanel() [1/2] CTreeBuilderPanel::CTreeBuilderPanel ( ) ◆ CTreeBuilderPanel() [2/2] CTreeBuilderPanel::CTreeBuilderPanel ( wxWindow *  parent, wxWindowID  id = ID_CTreeBuilderPanel, const wxPoint &  pos = wxDefaultPosition, const wxSize &  size = wxSize(400, 300), long  style = wxTAB_TRAVERSAL  ) ◆ CTreeBuilderParams() [1/2] CTreeBuilderParams::CTreeBuilderParams ( ) ◆ CTreeBuilderParams() [2/2] ◆ CTreeBuilderTool() CTreeBuilderTool::CTreeBuilderTool ( ) ◆ DebugDump()

Implements CDebugDumpable.

Definition at line 148 of file splign_params.cpp.

References CDebugDumpContext::Log(), CSplignParams::m_cDNA_strand, CSplignParams::m_CompPenalty, CSplignParams::m_DiscType, CSplignParams::m_EndGapDetect, CSplignParams::m_MaxGenomicExtent, CSplignParams::m_MaxIntron, CSplignParams::m_MinCompIdentity, CSplignParams::m_MinExonIdentity, CSplignParams::m_PolyADetect, and CDebugDumpContext::SetFrame().

◆ DECLARE_EVENT_MAP() [1/3] CMultiAlignView::DECLARE_EVENT_MAP ( ) private ◆ DECLARE_EVENT_MAP() [2/3] CNetBLAST_DMSearchForm::DECLARE_EVENT_MAP ( ) private ◆ DECLARE_EVENT_MAP() [3/3] CPhyTreeView::DECLARE_EVENT_MAP ( ) private ◆ DeleteJobDescriptors() void CNetBLASTUIDataSource::DeleteJobDescriptors ( TJobDescrVec &  descriptors ) ◆ DestroyView() void CMPCrossAlignView::DestroyView ( ) virtual ◆ DestroyViewWindow() [1/7] void CAlignSpanView::DestroyViewWindow ( ) virtual ◆ DestroyViewWindow() [2/7] void CAnnotCompareView::DestroyViewWindow ( ) virtual ◆ DestroyViewWindow() [3/7] void CCrossAlignView::DestroyViewWindow ( ) virtual ◆ DestroyViewWindow() [4/7] void CDotMatrixView::DestroyViewWindow ( ) virtual ◆ DestroyViewWindow() [5/7] void CMPCrossAlignView::DestroyViewWindow ( ) virtual ◆ DestroyViewWindow() [6/7] void CMultiAlignView::DestroyViewWindow ( ) virtual ◆ DestroyViewWindow() [7/7] void CPhyTreeView::DestroyViewWindow ( ) virtual ◆ DetachClient() ◆ DoTransition() [1/5] bool CBLASTToolManager::DoTransition ( EAction  action ) virtual

Performs transition if possible and returns true, otherwise the function shall warn the user about the problem preventing the transition (such as insufficient or invalid input) and return false.

Typically this function would take user input from the current panel, validate the input and go to the next state creating new UI panel if needed.

Implements IUIToolManager.

Definition at line 221 of file blast_tool_manager.cpp.

References _ASSERT, CBLASTToolManager::eCompleted, CBLASTToolManager::eInvalid, IUIToolManager::eNext, CBLASTToolManager::eOptions, CBLASTToolManager::eParams, ERR_POST, CException::GetMsg(), LOG_POST, CBLASTToolManager::m_OptionsPanel, CBLASTToolManager::m_ParamsPanel, CBLASTToolManager::m_State, NcbiErrorBox(), next(), CException::ReportAll(), CBLASTSearchOptionsPanel::SaveSettings(), Trace(), CBLASTSearchOptionsPanel::TransferDataFromWindow(), CBLASTSearchParamsPanel::TransferDataFromWindow(), CBLASTSearchOptionsPanel::TransferDataToWindow(), CBLASTSearchParamsPanel::TransferDataToWindow(), CBLASTToolManager::x_CreateOptionsPanelIfNeeded(), CBLASTToolManager::x_CreateParamsPanelIfNeeded(), CBLASTToolManager::x_InitProjectParams(), and CBLASTToolManager::x_ValidateParams().

◆ DoTransition() [2/5] bool CNetBLASTUILoadManager::DoTransition ( EAction  action ) virtual

Performs transition if possible and returns true, otherwise the function shall warn the user about the problem preventing the transition (such as insufficient or invalid input) and return false.

Typically this function would take user input from the current panel, validate the input and go to the next state creating new UI panel if needed.

Implements IUIToolManager.

Definition at line 152 of file net_blast_ui_load_manager.cpp.

References _ASSERT, IUIToolManager::eBack, CNetBLASTUILoadManager::eCompleted, IUIToolManager::eNext, CNetBLASTUILoadManager::eSelectProject, CNetBLASTUILoadManager::eSelectRID, CNetBLASTLoadOptionPanel::IsInputValid(), CNetBLASTUILoadManager::m_OptionPanel, CNetBLASTUILoadManager::m_ProjectSelPanel, CNetBLASTUILoadManager::m_State, and CProjectSelectorPanel::TransferDataFromWindow().

◆ DoTransition() [3/5]

Performs transition if possible and returns true, otherwise the function shall warn the user about the problem preventing the transition (such as insufficient or invalid input) and return false.

Typically this function would take user input from the current panel, validate the input and go to the next state creating new UI panel if needed.

Reimplemented from CAlgoToolManagerBase.

Definition at line 99 of file ngalign_tool.cpp.

References _ASSERT, CAlgoToolManagerBase::eCompleted, CAlgoToolManagerBase::eInvalid, IUIToolManager::eNext, CAlgoToolManagerBase::eParams, CAlgoToolManagerBase::eSelectProject, CNGAlignTool::m_Panel, CAlgoToolManagerBase::m_ProjectSelPanel, CAlgoToolManagerBase::m_State, next(), CNGAlignPanel::SaveSettings(), CProjectSelectorPanel::TransferDataFromWindow(), CProjectSelectorPanel::TransferDataToWindow(), CAlgoToolManagerBase::x_CreateProjectPanelIfNeeded(), CNGAlignTool::x_GetCurrentPage(), CNGAlignTool::x_GoFirstPage(), CNGAlignTool::x_GoLastPage(), CNGAlignTool::x_GoNextPage(), CNGAlignTool::x_GoPrevPage(), CNGAlignTool::x_IsFirstPage(), and CNGAlignTool::x_IsLastPage().

◆ DoTransition() [4/5]

Performs transition if possible and returns true, otherwise the function shall warn the user about the problem preventing the transition (such as insufficient or invalid input) and return false.

Typically this function would take user input from the current panel, validate the input and go to the next state creating new UI panel if needed.

Implements IUIToolManager.

Definition at line 156 of file psl_load_manager.cpp.

References _ASSERT, IUIToolManager::eBack, CPslLoadManager::eCompleted, IUIToolManager::eNext, CPslLoadManager::eParams, CPslParamsPanel::GetData(), CPslLoadManager::m_Params, CPslLoadManager::m_ParamsPanel, CPslLoadManager::m_State, and CPslParamsPanel::TransferDataFromWindow().

◆ DoTransition() [5/5] bool CTextAlignLoaderManager::DoTransition ( EAction  action ) virtual

Performs transition if possible and returns true, otherwise the function shall warn the user about the problem preventing the transition (such as insufficient or invalid input) and return false.

Typically this function would take user input from the current panel, validate the input and go to the next state creating new UI panel if needed.

Implements IUIToolManager.

Definition at line 153 of file text_align_load_manager.cpp.

References _ASSERT, IUIToolManager::eBack, CTextAlignLoaderManager::eCompleted, IUIToolManager::eNext, CTextAlignLoaderManager::eParams, CTextAlignParamsPanel::GetData(), CTextAlignLoaderManager::m_Params, CTextAlignLoaderManager::m_ParamsPanel, CTextAlignLoaderManager::m_State, and CTextAlignParamsPanel::TransferDataFromWindow().

◆ EditProperties() ◆ Execute()

Implements IExecuteUnit.

Definition at line 87 of file text_align_object_loader.cpp.

References file, CException::GetMsg(), CTextAlignObjectLoader::Init(), ICanceled::IsCanceled(), ITERATE, kEmptyStr, CTextAlignObjectLoader::LoadFromStream(), CTextAlignObjectLoader::m_FileNames, CTextAlignObjectLoader::m_Objects, ToStdString(), CException::what(), and CReportLoaderErrors::x_UpdateHTMLResults().

◆ Expand() void CBLAST_Dlg_Item::Expand ( bool  expand ) inline ◆ FindCompartments() void CBLASTParams::FindCompartments ( bool  req ) inline ◆ FindJobDescriptor() ◆ FromUserObject() [1/2] void CBLASTParams::FromUserObject ( const objects::CUser_object &  user_obj )

Definition at line 551 of file blast_search_params.cpp.

References CBLASTParams::eLocalDB, CBLASTParams::eNCBIDB, CBLASTParams::eSequences, CUser_field_Base::C_Data::GetBool(), CUser_field_Base::GetData(), CUser_object::GetField(), CUser_field_Base::C_Data::GetInt(), CUser_field_Base::C_Data::GetObject(), CBLASTParams::GetProgramByLabel(), CBLASTParams::GetProgramLabel(), CUser_field_Base::C_Data::GetStr(), kAdvParamsTag, kEntrezQueryTag, kJobTitleTag, kLocalDBLoader, kLocalNucDB, kLocalProtDB, kNucDBTag, kNucMRUDBsTag, kNucProgTag, kProtDBTag, kProtMRUDBsTag, kProtProgTag, kSubjectType, CBLASTParams::m_AdvancedParams, CBLASTParams::m_EntrezQuery, CBLASTParams::m_JobTitle, CBLASTParams::m_LocalDBLoader, CBLASTParams::m_LocalNucDB, CBLASTParams::m_LocalProtDB, CBLASTParams::m_NucDatabase, CBLASTParams::m_NucMRUDatabases, CBLASTParams::m_NucProgram, CBLASTParams::m_ProgToParams, CBLASTParams::m_ProtDatabase, CBLASTParams::m_ProtMRUDatabases, CBLASTParams::m_ProtProgram, CBLASTParams::m_SubjectType, NON_CONST_ITERATE, CMRUList< T >::SetItems(), val, and CBLASTParams::x_FromUserObject().

Referenced by CBLASTToolManager::LoadSettings().

◆ FromUserObject() [2/2] void CNetBlastJobDescriptor::FromUserObject ( const objects::CUser_object &  user_obj )

Definition at line 412 of file net_blast_job_descr.cpp.

References CNetBlastJobDescriptor::eInvalidState, CTime::GetTimeT(), kDescrTag, kErrorsTag, kRIDTag, kStateTag, kSubmitTimeTag, kTitleTag, CNetBlastJobDescriptor::m_Description, CNetBlastJobDescriptor::m_Errors, CNetBlastJobDescriptor::m_JobTitle, CNetBlastJobDescriptor::m_RID, CNetBlastJobDescriptor::m_State, and CNetBlastJobDescriptor::m_SubmitTime.

◆ GetAdvancedParams() [1/2] string & CBLASTParams::GetAdvancedParams ( ) ◆ GetAdvancedParams() [2/2] string CBLASTParams::GetAdvancedParams ( ) const ◆ GetAdvParams() [1/2] wxString CBLASTSearchParamsPanel::GetAdvParams ( ) const inline ◆ GetAdvParams() [2/2] wxString CNGAlignParams::GetAdvParams ( ) const inline ◆ GetAllRepeatLibs() ◆ GetAutoFlag() bool CMafftToolParams::GetAutoFlag ( ) const inline ◆ GetBandSize() int CNeedlemanWunschToolParams::GetBandSize ( ) const inline ◆ GetBestHit() bool CNGAlignParams::GetBestHit ( ) const inline ◆ GetBitmapResource() [1/14] ◆ GetBitmapResource() [2/14] wxBitmap CBLASTSearchOptionsPanel::GetBitmapResource ( const wxString &  name ) ◆ GetBitmapResource() [3/14] ◆ GetBitmapResource() [4/14] ◆ GetBitmapResource() [5/14] ◆ GetBitmapResource() [6/14] ◆ GetBitmapResource() [7/14] ◆ GetBitmapResource() [8/14] ◆ GetBitmapResource() [9/14] ◆ GetBitmapResource() [10/14] ◆ GetBitmapResource() [11/14] ◆ GetBitmapResource() [12/14] wxBitmap CMuscleToolPanel::GetBitmapResource ( const wxString &  name ) ◆ GetBitmapResource() [13/14] ◆ GetBitmapResource() [14/14] ◆ GetBLASTDataSource() ◆ GetBlastParams() wxString CFindOverlapParams::GetBlastParams ( ) const inline ◆ GetCategory() string CBLASTToolManager::GetCategory ( ) virtual ◆ GetCDNASeqs() ◆ GetCDNAStrand() int CSplignParams::GetCDNAStrand ( ) const inline ◆ GetChildByLabel() ◆ GetChildItems() ◆ GetClustalOmegaExecutable() wxString CClustalOmegaToolParams::GetClustalOmegaExecutable ( ) const ◆ GetClustalOmegaPath() wxString CClustalOmegaToolParams::GetClustalOmegaPath ( ) const inline ◆ GetClustalWExecutable() wxString CClustalwToolParams::GetClustalWExecutable ( ) const ◆ GetClustalWPath() wxString CClustalwToolParams::GetClustalWPath ( ) const inline ◆ GetCommandLine() [1/5] wxString CClustalOmegaToolParams::GetCommandLine ( void  ) const inline ◆ GetCommandLine() [2/5] wxString CClustalwToolParams::GetCommandLine ( void  ) const inline ◆ GetCommandLine() [3/5] wxString CKalignToolParams::GetCommandLine ( void  ) const inline ◆ GetCommandLine() [4/5] wxString CMafftToolParams::GetCommandLine ( void  ) const inline ◆ GetCommandLine() [5/5] wxString CMuscleToolParams::GetCommandLine ( void  ) const inline ◆ GetCompleted() bool CNetBlastDMSearchFormPanel::GetCompleted ( ) const inline ◆ GetCompPenalty() double CSplignParams::GetCompPenalty ( ) const inline ◆ GetConstructMethod() wxString CTreeBuilderParams::GetConstructMethod ( ) const inline ◆ GetCurrDatabase() [1/2] string & CBLASTParams::GetCurrDatabase ( ) ◆ GetCurrDatabase() [2/2] ◆ GetCurrentPanel() [1/5] wxPanel * CBLASTToolManager::GetCurrentPanel ( ) virtual ◆ GetCurrentPanel() [2/5] wxPanel * CNetBLASTUILoadManager::GetCurrentPanel ( ) virtual

Return the panel corresponding to the current state of Tool Manager.

Implements IUIToolManager.

Definition at line 99 of file net_blast_ui_load_manager.cpp.

References CNetBLASTUILoadManager::eSelectProject, CNetBLASTUILoadManager::eSelectRID, IServiceLocator::GetServiceByType(), CNetBLASTUILoadManager::m_OptionPanel, CNetBLASTUILoadManager::m_ParentWindow, CNetBLASTUILoadManager::m_ProjectParams, CNetBLASTUILoadManager::m_ProjectSelPanel, CNetBLASTUILoadManager::m_SavedInput, CNetBLASTUILoadManager::m_SrvLocator, CNetBLASTUILoadManager::m_State, NULL, CNetBLASTLoadOptionPanel::SetInput(), CProjectSelectorPanel::SetParams(), CProjectSelectorPanel::SetProjectService(), and CProjectSelectorPanel::TransferDataToWindow().

◆ GetCurrentPanel() [3/5] wxPanel * CNGAlignTool::GetCurrentPanel ( ) protectedvirtual ◆ GetCurrentPanel() [4/5] wxPanel * CPslLoadManager::GetCurrentPanel ( ) virtual ◆ GetCurrentPanel() [5/5] wxPanel * CTextAlignLoaderManager::GetCurrentPanel ( ) virtual ◆ GetCurrMRUDatabases() ◆ GetCurrParams() [1/2]

returns params for the current program

Definition at line 441 of file blast_search_params.cpp.

References _ASSERT, map_checker< Container >::end(), map_checker< Container >::find(), CBLASTParams::GetCurrProgram(), and CBLASTParams::m_ProgToParams.

Referenced by CBLASTParams::GetCurrParams(), CBLASTParams::PrintParams(), CBLASTSearchParamsPanel::TaxonsLoaded(), CBLASTParams::ToArgVec(), CBLASTSearchParamsPanel::TransferDataFromWindow(), CBLASTSearchParamsPanel::TransferDataToWindow(), CBLASTSeqToolJob::x_CreateProjectItems(), and CBLASTSearchParamsPanel::x_InitTaxons().

◆ GetCurrParams() [2/2] ◆ GetCurrProgram() [1/2]

returns the current program for the currently selected input type

Definition at line 299 of file blast_search_params.cpp.

References CBLASTParams::GetProgram(), and CBLASTParams::m_NucInput.

Referenced by CBLASTParams::GetCurrDatabase(), CBLASTParams::GetCurrMRUDatabases(), CBLASTParams::GetCurrParams(), CBLASTParams::IsSubjNucInput(), CBLASTSearchOptionsPanel::OnProgramComboSelected(), CBLASTParams::PrintParams(), CBLASTParams::ResetCurrParams(), CBLASTParams::ToArgs(), CBLASTParams::ToArgVec(), CBLASTParams::ToArgVecBlastOptions(), CBLASTParams::ToBlastOptions(), CBLASTSearchOptionsPanel::TransferDataFromWindow(), CBLASTSearchParamsPanel::TransferDataFromWindow(), CBLASTSearchParamsPanel::TransferDataToWindow(), CBLASTSeqToolJob::x_CreateProjectItems(), CBLASTSearchParamsPanel::x_HideShowInputs(), CBLASTSearchOptionsPanel::x_OnInputTypeChanged(), and CBLASTSearchOptionsPanel::x_UpdateDBCombo().

◆ GetCurrProgram() [2/2] ◆ GetData() [1/10] ◆ GetData() [2/10] ◆ GetData() [3/10] ◆ GetData() [4/10] ◆ GetData() [5/10] ◆ GetData() [6/10] ◆ GetData() [7/10] ◆ GetData() [8/10] ◆ GetData() [9/10] ◆ GetData() [10/10] ◆ GetDatabase() [1/2] string & CBLASTParams::GetDatabase ( bool  nuc_db ) ◆ GetDatabase() [2/2] ◆ GetDbGeneticCode() wxString CBLASTSearchParamsPanel::GetDbGeneticCode ( void  ) const inline ◆ GetDbNames() void CNetBLAST_DMSearchTool::GetDbNames ( vector< string > &  name ) ◆ GetDefaultCommand() int CNetBLASTUIDataSource::GetDefaultCommand ( void  ) virtual ◆ GetDescr() [1/4] ◆ GetDescr() [2/4] ◆ GetDescr() [3/4] string CNetBlastSubmittingJob::GetDescr ( ) const virtual ◆ GetDescr() [4/4] string CNetBlastMonitoringJob::GetDescr ( ) const virtual ◆ GetDescription() [1/3] string CNetBLAST_DMSearchTool::GetDescription ( ) const virtual ◆ GetDescription() [2/3] string CNetBlastJobDescriptor::GetDescription ( void  ) const ◆ GetDescription() [3/3] string CTextAlignObjectLoader::GetDescription ( void  ) const virtual ◆ GetDescriptor() [1/4] ◆ GetDescriptor() [2/4] ◆ GetDescriptor() [3/4] ◆ GetDescriptor() [4/4] ◆ GetDescriptors() void CNetBlastSubmittingJob::GetDescriptors ( TDescriptors &  descriptors ) ◆ GetDiscType() int CSplignParams::GetDiscType ( ) const inline ◆ GetDistanceMethod() wxString CTreeBuilderParams::GetDistanceMethod ( ) const inline ◆ GetEndGapDetect() bool CSplignParams::GetEndGapDetect ( ) const inline ◆ GetEntrezQuery() [1/2] string & CBLASTParams::GetEntrezQuery ( void  ) ◆ GetEntrezQuery() [2/2] string CBLASTParams::GetEntrezQuery ( void  ) const ◆ GetError() [1/2] ◆ GetError() [2/2] ◆ GetErrors() [1/3] string CNetBlastJobDescriptor::GetErrors ( void  ) const ◆ GetErrors() [2/3] void CNetBlastSubmittingJob::GetErrors ( vector< string > &  errors ) const ◆ GetErrors() [3/3] void CNetBlastLoadingJob::GetErrors ( vector< string > &  errors ) const ◆ GetEValue() [1/2] double CBLASTSearchParamsPanel::GetEValue ( void  ) const inline ◆ GetEValue() [2/2] double CNGAlignParams::GetEValue ( void  ) const inline ◆ GetExecuteUnit() [1/2] ◆ GetExecuteUnit() [2/2] ◆ GetExpired() bool CNetBlastDMSearchFormPanel::GetExpired ( ) const inline ◆ GetExtensionIdentifier() [1/30] string CAlignSpanViewFactory::GetExtensionIdentifier ( ) const virtual

returns the unique human-readable identifier for the extension the id should use lowercase letters separated by underscores - "like_this"

Implements IExtension.

Definition at line 624 of file align_span_view.cpp.

◆ GetExtensionIdentifier() [2/30] string CAnnotCompareViewFactory::GetExtensionIdentifier ( ) const virtual ◆ GetExtensionIdentifier() [3/30] string CBLASTToolManager::GetExtensionIdentifier ( ) const virtual

returns the unique human-readable identifier for the extension the id should use lowercase letters separated by underscores - "like_this"

Implements IExtension.

Definition at line 77 of file blast_tool_manager.cpp.

◆ GetExtensionIdentifier() [4/30] string CCleanupAlignmentsToolManager::GetExtensionIdentifier ( ) const virtual ◆ GetExtensionIdentifier() [5/30] string CClustalOmegaTool::GetExtensionIdentifier ( ) const virtual

returns the unique human-readable identifier for the extension the id should use lowercase letters separated by underscores - "like_this"

Implements CAlgoToolManagerBase.

Definition at line 58 of file clustal_omega_tool.cpp.

◆ GetExtensionIdentifier() [6/30] string CClustalwTool::GetExtensionIdentifier ( ) const virtual

returns the unique human-readable identifier for the extension the id should use lowercase letters separated by underscores - "like_this"

Implements CAlgoToolManagerBase.

Definition at line 58 of file clustalw_tool.cpp.

◆ GetExtensionIdentifier() [7/30] string CCreateGeneModelToolManager::GetExtensionIdentifier ( ) const virtual ◆ GetExtensionIdentifier() [8/30] string CCrossAlignViewFactory::GetExtensionIdentifier ( ) const virtual ◆ GetExtensionIdentifier() [9/30] string CDotMatrixViewFactory::GetExtensionIdentifier ( ) const virtual

returns the unique human-readable identifier for the extension the id should use lowercase letters separated by underscores - "like_this"

Implements IExtension.

Definition at line 377 of file dot_matrix_view.cpp.

◆ GetExtensionIdentifier() [10/30] string CFindOverlapTool::GetExtensionIdentifier ( ) const virtual

returns the unique human-readable identifier for the extension the id should use lowercase letters separated by underscores - "like_this"

Implements CAlgoToolManagerBase.

Definition at line 84 of file find_overlap_tool.cpp.

◆ GetExtensionIdentifier() [11/30] string CGroupAlignmentsToolManager::GetExtensionIdentifier ( ) const virtual ◆ GetExtensionIdentifier() [12/30] string CKalignTool::GetExtensionIdentifier ( ) const virtual

returns the unique human-readable identifier for the extension the id should use lowercase letters separated by underscores - "like_this"

Implements CAlgoToolManagerBase.

Definition at line 57 of file kalign_tool.cpp.

◆ GetExtensionIdentifier() [13/30] string CMafftTool::GetExtensionIdentifier ( ) const virtual

returns the unique human-readable identifier for the extension the id should use lowercase letters separated by underscores - "like_this"

Implements CAlgoToolManagerBase.

Definition at line 57 of file mafft_tool.cpp.

◆ GetExtensionIdentifier() [14/30] string CMergeAlignmentsToolManager::GetExtensionIdentifier ( ) const virtual ◆ GetExtensionIdentifier() [15/30] string CMPCrossAlignViewFactory::GetExtensionIdentifier ( ) const virtual ◆ GetExtensionIdentifier() [16/30] string CMultiAlignViewFactory::GetExtensionIdentifier ( ) const virtual ◆ GetExtensionIdentifier() [17/30] string CMuscleTool::GetExtensionIdentifier ( ) const virtual

returns the unique human-readable identifier for the extension the id should use lowercase letters separated by underscores - "like_this"

Implements CAlgoToolManagerBase.

Definition at line 57 of file muscle_tool.cpp.

◆ GetExtensionIdentifier() [18/30] string CNetBLAST_DMSearchTool::GetExtensionIdentifier ( ) const virtual

returns the unique human-readable identifier for the extension the id should use lowercase letters separated by underscores - "like_this"

Implements IExtension.

Definition at line 215 of file net_blast_dm_search_tool.cpp.

◆ GetExtensionIdentifier() [19/30] string CNetBLASTUIDataSource::GetExtensionIdentifier ( ) const virtual

returns the unique human-readable identifier for the extension the id should use lowercase letters separated by underscores - "like_this"

Implements IExtension.

Definition at line 159 of file net_blast_ui_data_source.cpp.

◆ GetExtensionIdentifier() [20/30] string CNetBLASTUIDataSourceType::GetExtensionIdentifier ( ) const virtual

returns the unique human-readable identifier for the extension the id should use lowercase letters separated by underscores - "like_this"

Implements IExtension.

Definition at line 655 of file net_blast_ui_data_source.cpp.

◆ GetExtensionIdentifier() [21/30] string CNGAlignTool::GetExtensionIdentifier ( ) const virtual

returns the unique human-readable identifier for the extension the id should use lowercase letters separated by underscores - "like_this"

Implements CAlgoToolManagerBase.

Definition at line 67 of file ngalign_tool.cpp.

◆ GetExtensionIdentifier() [22/30] string CPhyTreeViewFactory::GetExtensionIdentifier ( ) const virtual ◆ GetExtensionIdentifier() [23/30] string CProSplignTool::GetExtensionIdentifier ( ) const virtual

returns the unique human-readable identifier for the extension the id should use lowercase letters separated by underscores - "like_this"

Implements CAlgoToolManagerBase.

Definition at line 127 of file prosplign_tool.cpp.

◆ GetExtensionIdentifier() [24/30] string CSplignTool::GetExtensionIdentifier ( ) const virtual

returns the unique human-readable identifier for the extension the id should use lowercase letters separated by underscores - "like_this"

Implements CAlgoToolManagerBase.

Definition at line 73 of file splign_tool.cpp.

◆ GetExtensionIdentifier() [25/30] string CCommonTaxTreeTool::GetExtensionIdentifier ( ) const virtual

returns the unique human-readable identifier for the extension the id should use lowercase letters separated by underscores - "like_this"

Implements CAlgoToolManagerBase.

Definition at line 58 of file taxtree_tool.cpp.

◆ GetExtensionIdentifier() [26/30] string CTreeBuilderTool::GetExtensionIdentifier ( ) const virtual

returns the unique human-readable identifier for the extension the id should use lowercase letters separated by underscores - "like_this"

Implements CAlgoToolManagerBase.

Definition at line 97 of file tree_builder_tool.cpp.

◆ GetExtensionIdentifier() [27/30] string CAdvancedCleanupTool::GetExtensionIdentifier ( ) const virtual ◆ GetExtensionIdentifier() [28/30] string CCreateNeedlemanWunschToolManager::GetExtensionIdentifier ( ) const virtual ◆ GetExtensionIdentifier() [29/30] string CPslLoadManager::GetExtensionIdentifier ( ) const virtual

returns the unique human-readable identifier for the extension the id should use lowercase letters separated by underscores - "like_this"

Implements IExtension.

Definition at line 228 of file psl_load_manager.cpp.

◆ GetExtensionIdentifier() [30/30] string CTextAlignLoaderManager::GetExtensionIdentifier ( ) const virtual

returns the unique human-readable identifier for the extension the id should use lowercase letters separated by underscores - "like_this"

Implements IExtension.

Definition at line 229 of file text_align_load_manager.cpp.

◆ GetExtensionLabel() [1/30] string CAlignSpanViewFactory::GetExtensionLabel ( ) const virtual

returns a displayable label for this extension ( please capitalize the key words - "My Extension" )

Implements IExtension.

Definition at line 631 of file align_span_view.cpp.

◆ GetExtensionLabel() [2/30] string CAnnotCompareViewFactory::GetExtensionLabel ( ) const virtual

returns a displayable label for this extension ( please capitalize the key words - "My Extension" )

Implements IExtension.

Definition at line 348 of file annot_compare_view.cpp.

◆ GetExtensionLabel() [3/30] string CBLASTToolManager::GetExtensionLabel ( ) const virtual

returns a displayable label for this extension ( please capitalize the key words - "My Extension" )

Implements IExtension.

Definition at line 83 of file blast_tool_manager.cpp.

◆ GetExtensionLabel() [4/30] string CCleanupAlignmentsToolManager::GetExtensionLabel ( ) const virtual ◆ GetExtensionLabel() [5/30] string CClustalOmegaTool::GetExtensionLabel ( ) const virtual ◆ GetExtensionLabel() [6/30] string CClustalwTool::GetExtensionLabel ( ) const virtual ◆ GetExtensionLabel() [7/30] string CCreateGeneModelToolManager::GetExtensionLabel ( ) const virtual ◆ GetExtensionLabel() [8/30] string CCrossAlignViewFactory::GetExtensionLabel ( ) const virtual

returns a displayable label for this extension ( please capitalize the key words - "My Extension" )

Implements IExtension.

Definition at line 372 of file cross_align_view.cpp.

◆ GetExtensionLabel() [9/30] string CDotMatrixViewFactory::GetExtensionLabel ( ) const virtual

returns a displayable label for this extension ( please capitalize the key words - "My Extension" )

Implements IExtension.

Definition at line 383 of file dot_matrix_view.cpp.

◆ GetExtensionLabel() [10/30] string CFindOverlapTool::GetExtensionLabel ( ) const virtual ◆ GetExtensionLabel() [11/30] string CGroupAlignmentsToolManager::GetExtensionLabel ( ) const virtual ◆ GetExtensionLabel() [12/30] string CKalignTool::GetExtensionLabel ( ) const virtual ◆ GetExtensionLabel() [13/30] string CMafftTool::GetExtensionLabel ( ) const virtual ◆ GetExtensionLabel() [14/30] string CMergeAlignmentsToolManager::GetExtensionLabel ( ) const virtual ◆ GetExtensionLabel() [15/30] string CMPCrossAlignViewFactory::GetExtensionLabel ( ) const virtual ◆ GetExtensionLabel() [16/30] string CMultiAlignViewFactory::GetExtensionLabel ( ) const virtual

returns a displayable label for this extension ( please capitalize the key words - "My Extension" )

Implements IExtension.

Definition at line 599 of file multi_align_view.cpp.

◆ GetExtensionLabel() [17/30] string CMuscleTool::GetExtensionLabel ( ) const virtual ◆ GetExtensionLabel() [18/30] string CNetBLAST_DMSearchTool::GetExtensionLabel ( ) const virtual ◆ GetExtensionLabel() [19/30] string CNetBLASTUIDataSource::GetExtensionLabel ( ) const virtual ◆ GetExtensionLabel() [20/30] string CNetBLASTUIDataSourceType::GetExtensionLabel ( ) const virtual ◆ GetExtensionLabel() [21/30] string CNGAlignTool::GetExtensionLabel ( ) const virtual ◆ GetExtensionLabel() [22/30] string CPhyTreeViewFactory::GetExtensionLabel ( ) const virtual

returns a displayable label for this extension ( please capitalize the key words - "My Extension" )

Implements IExtension.

Definition at line 1836 of file phy_tree_view.cpp.

◆ GetExtensionLabel() [23/30] string CProSplignTool::GetExtensionLabel ( ) const virtual ◆ GetExtensionLabel() [24/30] string CSplignTool::GetExtensionLabel ( ) const virtual ◆ GetExtensionLabel() [25/30] string CCommonTaxTreeTool::GetExtensionLabel ( ) const virtual ◆ GetExtensionLabel() [26/30] string CTreeBuilderTool::GetExtensionLabel ( ) const virtual ◆ GetExtensionLabel() [27/30] string CAdvancedCleanupTool::GetExtensionLabel ( ) const virtual ◆ GetExtensionLabel() [28/30] string CCreateNeedlemanWunschToolManager::GetExtensionLabel ( ) const virtual ◆ GetExtensionLabel() [29/30] string CPslLoadManager::GetExtensionLabel ( ) const virtual

returns a displayable label for this extension ( please capitalize the key words - "My Extension" )

Implements IExtension.

Definition at line 234 of file psl_load_manager.cpp.

◆ GetExtensionLabel() [30/30] string CTextAlignLoaderManager::GetExtensionLabel ( ) const virtual ◆ GetFailed() bool CNetBlastDMSearchFormPanel::GetFailed ( ) const inline ◆ GetFileLoaderId() [1/2] virtual string CPslLoadManager::GetFileLoaderId ( ) const inlinevirtual ◆ GetFileLoaderId() [2/2] virtual string CTextAlignLoaderManager::GetFileLoaderId ( ) const inlinevirtual ◆ GetFilenames() [1/2] void CPslLoadManager::GetFilenames ( vector< wxString > &  filenames ) const virtual ◆ GetFilenames() [2/2] void CTextAlignLoaderManager::GetFilenames ( vector< wxString > &  filenames ) const virtual ◆ GetFilterLowComplex() bool CBLASTSearchParamsPanel::GetFilterLowComplex ( ) const inline ◆ GetFilterMode() int CNGAlignParams::GetFilterMode ( ) const inline ◆ GetFilterQuality() int CFindOverlapParams::GetFilterQuality ( ) const inline ◆ GetFirstPage() [1/2] ◆ GetFirstPage() [2/2] virtual IWizardPage* CTextAlignLoaderManager::GetFirstPage ( ) inlinevirtual ◆ GetFirstSeqFreeEnds() int CNeedlemanWunschToolParams::GetFirstSeqFreeEnds ( ) const inline ◆ GetFlags() ◆ GetFormatWildcard() [1/4] wxString CPslLoadManager::GetFormatWildcard ( ) virtual ◆ GetFormatWildcard() [2/4] wxString CTextAlignLoaderManager::GetFormatWildcard ( ) virtual ◆ GetFormatWildcard() [3/4] wxString CPslLoadManager::GetFormatWildcard ( ) const virtual ◆ GetFormatWildcard() [4/4] wxString CTextAlignLoaderManager::GetFormatWildcard ( ) const virtual ◆ GetGapExtendCost() int CNeedlemanWunschToolParams::GetGapExtendCost ( ) const inline ◆ GetGapOpenCost() int CNeedlemanWunschToolParams::GetGapOpenCost ( ) const inline ◆ GetGenerateTree() [1/3] bool CClustalOmegaToolParams::GetGenerateTree ( ) const inline ◆ GetGenerateTree() [2/3] bool CClustalwToolParams::GetGenerateTree ( ) const inline ◆ GetGenerateTree() [3/3] bool CMuscleToolParams::GetGenerateTree ( ) const inline ◆ GetGeneticCode() wxString CBLASTSearchParamsPanel::GetGeneticCode ( ) const inline ◆ GetGeneticCodeByLabel() ◆ GetGeneticCodeLabel() string CBLASTParams::GetGeneticCodeLabel ( int  code_id ) static ◆ GetGeneticCodeLabels() void CBLASTParams::GetGeneticCodeLabels ( vector< string > &  labels ) static ◆ GetGenomicSeq() ◆ GetIconResource() [1/14] ◆ GetIconResource() [2/14] ◆ GetIconResource() [3/14] ◆ GetIconResource() [4/14] ◆ GetIconResource() [5/14] ◆ GetIconResource() [6/14] ◆ GetIconResource() [7/14] ◆ GetIconResource() [8/14] ◆ GetIconResource() [9/14] ◆ GetIconResource() [10/14] ◆ GetIconResource() [11/14] ◆ GetIconResource() [12/14] ◆ GetIconResource() [13/14] ◆ GetIconResource() [14/14] ◆ GetId() const wxTreeItemId& CBLAST_Dlg_Item::GetId ( void  ) const inline ◆ GetID() ◆ GetInput() string CNetBLASTLoadOptionPanel::GetInput ( ) const ◆ GetJobDescriptors() void CNetBLASTUIDataSource::GetJobDescriptors ( TJobDescrVec &  descriptors ) ◆ GetJobTitle() [1/5] string & CBLASTParams::GetJobTitle ( ) ◆ GetJobTitle() [2/5] string CBLASTParams::GetJobTitle ( ) const ◆ GetJobTitle() [3/5] wxString CBLASTSearchParamsPanel::GetJobTitle ( ) const inline ◆ GetJobTitle() [4/5] string CNetBlastJobDescriptor::GetJobTitle ( ) const ◆ GetJobTitle() [5/5] wxString CNGAlignParams::GetJobTitle ( ) const inline ◆ GetKalignExecutable() wxString CKalignToolParams::GetKalignExecutable ( ) const ◆ GetKalignPath() wxString CKalignToolParams::GetKalignPath ( ) const inline ◆ GetLabel() [1/3] wxString CBLAST_Dlg_Item::GetLabel ( void  ) const ◆ GetLabel() [2/3] string CPslLoadManager::GetLabel ( void  ) const virtual ◆ GetLabel() [3/3] string CTextAlignLoaderManager::GetLabel ( void  ) const virtual ◆ GetLeafLabels() wxString CTreeBuilderParams::GetLeafLabels ( ) const inline ◆ GetLoadManager() ◆ GetLocalDBLoader() bool CBLASTParams::GetLocalDBLoader ( ) const inline ◆ GetLocalNucDB() string CBLASTParams::GetLocalNucDB ( ) const inline ◆ GetLocalProtDB() string CBLASTParams::GetLocalProtDB ( ) const inline ◆ GetMafftExecutable() wxString CMafftToolParams::GetMafftExecutable ( ) const ◆ GetMafftPath() wxString CMafftToolParams::GetMafftPath ( ) const inline ◆ GetMainObject() ◆ GetMatchCost() int CNeedlemanWunschToolParams::GetMatchCost ( ) const inline ◆ GetMaxGenomicExtent() long CSplignParams::GetMaxGenomicExtent ( void  ) const inline ◆ GetMaxIntron() long CSplignParams::GetMaxIntron ( void  ) const inline ◆ GetMaxPanel() [1/10] wxPanel * CBLASTToolManager::GetMaxPanel ( ) virtual ◆ GetMaxPanel() [2/10] wxPanel * CClustalOmegaTool::GetMaxPanel ( ) virtual ◆ GetMaxPanel() [3/10] wxPanel * CClustalwTool::GetMaxPanel ( ) virtual ◆ GetMaxPanel() [4/10] wxPanel * CKalignTool::GetMaxPanel ( ) virtual ◆ GetMaxPanel() [5/10] wxPanel * CMafftTool::GetMaxPanel ( ) virtual ◆ GetMaxPanel() [6/10] wxPanel * CMuscleTool::GetMaxPanel ( ) virtual ◆ GetMaxPanel() [7/10] wxPanel * CProSplignTool::GetMaxPanel ( ) virtual ◆ GetMaxPanel() [8/10] wxPanel * CSplignTool::GetMaxPanel ( ) virtual ◆ GetMaxPanel() [9/10] wxPanel * CCommonTaxTreeTool::GetMaxPanel ( ) virtual ◆ GetMaxPanel() [10/10] wxPanel * CAdvancedCleanupTool::GetMaxPanel ( ) virtual ◆ GetMaxSlop() wxString CFindOverlapParams::GetMaxSlop ( ) const inline ◆ GetMenu() [1/2]

returns a menu with commands applicable to the objects and optional command handler for the commands caller assumes ownership of the returned objects

Implements IObjectCmdContributor.

Definition at line 307 of file net_blast_ui_data_source.cpp.

References CUICommandRegistry::AppendMenuItem(), CNetBLASTUIDataSource::CNetBlastDSEvtHandler, eCmdDeleteBlastJobs, eCmdMonitorBlastJobs, eCmdRetriveBlastJobs, CNetBlastJobDescriptor::eCompleted, CNetBlastJobDescriptor::eRetrieved, CNetBlastJobDescriptor::eSubmitted, CUICommandRegistry::GetInstance(), CNetBlastJobDescriptor::GetState(), NON_CONST_ITERATE, NULL, and wxT.

◆ GetMenu() [2/2]

for the given set of items returns a contribution

Implements IExplorerItemCmdContributor.

Definition at line 364 of file net_blast_ui_data_source.cpp.

References CUICommandRegistry::AppendMenuItem(), CNetBLASTUIDataSource::CNetBlastDSEvtHandler, eCmdExploreNetBLAST, eCmdLoadRIDs, PT::eDataSource, PT::TPTItem< TData, Type >::GetData(), CUICommandRegistry::GetInstance(), CRef< C, Locker >::GetPointer(), PT::CItem::GetType(), and wxT.

◆ GetMenuDef() ◆ GetMinCompIdentity() double CSplignParams::GetMinCompIdentity ( ) const inline ◆ GetMinExonIdentity() double CSplignParams::GetMinExonIdentity ( void  ) const inline ◆ GetMismatchCost() int CNeedlemanWunschToolParams::GetMismatchCost ( ) const inline ◆ GetMRUDatabases() ◆ GetMuscleExecutable() wxString CMuscleToolParams::GetMuscleExecutable ( ) const ◆ GetMusclePath() wxString CMuscleToolParams::GetMusclePath ( ) const inline ◆ GetName() string CNetBLAST_DMSearchTool::GetName ( ) const virtual ◆ GetNumrow() ◆ GetObject() ◆ GetObjects() [1/8] ◆ GetObjects() [2/8] ◆ GetObjects() [3/8] ◆ GetObjects() [4/8] ◆ GetObjects() [5/8] ◆ GetObjects() [6/8] ◆ GetObjects() [7/8] ◆ GetObjects() [8/8] ◆ GetOpenViewManager() [1/2] ◆ GetOpenViewManager() [2/2] ◆ GetOptionsPage() virtual IWizardPage* CTextAlignLoaderManager::GetOptionsPage ( ) inlinevirtual ◆ GetPanel() [1/2] wxPanel * CPslLoadManager::CPage::GetPanel ( ) virtual ◆ GetPanel() [2/2] wxPanel * CTextAlignLoaderManager::CPage::GetPanel ( ) virtual ◆ GetParent() ◆ GetPath() ◆ GetPolyADetect() bool CSplignParams::GetPolyADetect ( ) const inline ◆ GetProgram() [1/2] ◆ GetProgram() [2/2] ◆ GetProgramByLabel() ◆ GetProgramLabel() ◆ GetProgramLabels() void CBLASTParams::GetProgramLabels ( bool  nuc_input, vector< string > &  labels  ) static ◆ GetProgress() [1/3] ◆ GetProgress() [2/3] ◆ GetProgress() [3/3] ◆ GetProjectViewTypeDescriptor() [1/7] ◆ GetProjectViewTypeDescriptor() [2/7] ◆ GetProjectViewTypeDescriptor() [3/7] ◆ GetProjectViewTypeDescriptor() [4/7] ◆ GetProjectViewTypeDescriptor() [5/7] ◆ GetProjectViewTypeDescriptor() [6/7] ◆ GetProjectViewTypeDescriptor() [7/7] ◆ GetQueries() [1/2] ◆ GetQueries() [2/2] ◆ GetQuietFlag() [1/2] bool CKalignToolParams::GetQuietFlag ( ) const inline ◆ GetQuietFlag() [2/2] bool CMafftToolParams::GetQuietFlag ( ) const inline ◆ GetRemoteBlast() CRef< blast::CRemoteBlast > CNetBlastJobDescriptor::GetRemoteBlast ( ) ◆ GetRepeatDb() ◆ GetRepeatLib() ◆ GetResult() [1/2]

Returns the Job Result.

Derive your own object from CObject and return it from your Job class. Result shall be returned only if Job finished succesfully.

Implements IAppJob.

Definition at line 223 of file blast_jobs.cpp.

◆ GetResult() [2/2]

Returns the Job Result.

Derive your own object from CObject and return it from your Job class. Result shall be returned only if Job finished succesfully.

Implements IAppJob.

Definition at line 451 of file blast_jobs.cpp.

◆ GetRetrieved() bool CNetBlastDMSearchFormPanel::GetRetrieved ( ) const inline ◆ GetRID() string CNetBlastJobDescriptor::GetRID ( void  ) const ◆ GetRIDs() void CNetBLASTLoadOptionPanel::GetRIDs ( vector< string > &  rids ) ◆ GetScheme() ◆ GetScoringMethod() int CMuscleToolParams::GetScoringMethod ( ) const inline ◆ GetSearchValue() wxString CNetBlastDMSearchFormPanel::GetSearchValue ( ) const inline ◆ GetSecondSeqFreeEnds() int CNeedlemanWunschToolParams::GetSecondSeqFreeEnds ( ) const inline ◆ GetSelectedDatabases() void CBLAST_DB_Dialog::GetSelectedDatabases ( vector< string > &  databases ) ◆ GetSelection() [1/14] ◆ GetSelection() [2/14] ◆ GetSelection() [3/14] ◆ GetSelection() [4/14] ◆ GetSelection() [5/14] ◆ GetSelection() [6/14]

get selection for broadcasting

Reimplemented from CProjectView.

Definition at line 500 of file multi_align_view.cpp.

References CSelectionEvent::AddObjectSelection(), CSelectionEvent::AddRangeSelection(), CRef< C, Locker >::GetPointer(), CAlnMultiWidget::GetSelectedRows(), ITERATE, CMultiAlignView::m_AlnWidget, CMultiAlignView::m_DataSource, row, CSelectionEvent::sm_MatchAlnLocs, and CMultiAlignView::x_GetSeqRangeSelection().

◆ GetSelection() [7/14]

get selection for broadcasting

Reimplemented from CProjectView.

Definition at line 1144 of file phy_tree_view.cpp.

References CSelectionEvent::AddIndexed(), CSelectionEvent::AddObjectSelection(), CSelectionEvent::AddTaxIDSelection(), CPhyloTreeDataSource::GetDictionary(), CPhyloTree::GetExplicitlySelectedIDs(), CBioTreeSelection::GetExplicitlySelectedNodeIds(), CBioTreeFeatureDictionary::GetId(), CTreeModel< TNode >::GetNode(), CBioTreeSelection::GetNodeIds(), CRef< C, Locker >::GetPointer(), CPhyloTree::GetSelected(), CPhyloTree::GetSelectedIDs(), CPhyloTreeDataSource::GetTree(), CPhyTreeView::GetWidget(), CBioTreeFeatureDictionary::HasFeature(), ITERATE, CPhyTreeView::m_BioTreeContainer, CPhyTreeView::m_DataSource, n, NStr::StringToUInt(), and CProjectViewBase::x_HasProject().

◆ GetSelection() [8/14]

shall return data objects representing selected things, return one data object for every selected thing.

Implementation shall not clear the container as it can be used for accumulating objects.

Reimplemented from CProjectView.

Definition at line 479 of file align_span_view.cpp.

References _ASSERT, GetIdHandle(), CProjectViewBase::GetScope(), CAlnSpanWidget::GetSelection(), CRef< C, Locker >::IsNull(), ITERATE, CAlignSpanView::m_AlnWidget, NULL, CSeq_loc::SetId(), CSeq_loc::SetInt(), and CProjectViewBase::x_HasProject().

◆ GetSelection() [9/14]

shall return data objects representing selected things, return one data object for every selected thing.

Implementation shall not clear the container as it can be used for accumulating objects.

Reimplemented from CProjectView.

Definition at line 194 of file annot_compare_view.cpp.

◆ GetSelection() [10/14]

shall return data objects representing selected things, return one data object for every selected thing.

Implementation shall not clear the container as it can be used for accumulating objects.

Reimplemented from CProjectView.

Definition at line 198 of file cross_align_view.cpp.

References _ASSERT, CSeqUtils::CreateSeq_loc(), CRangeCollection< Position >::empty(), CCrossAlnWidget::GetObjectSelection(), CCrossAlnWidget::GetQueryRangeSelection(), CCrossAlnWidget::GetSubjectRangeSelection(), ITERATE, CCrossAlignView::m_AlnWidget, CCrossAlignView::m_DataSource, CProjectViewBase::x_GetScope(), and CProjectViewBase::x_HasProject().

◆ GetSelection() [11/14]

shall return data objects representing selected things, return one data object for every selected thing.

Implementation shall not clear the container as it can be used for accumulating objects.

Reimplemented from CProjectView.

Definition at line 205 of file dot_matrix_view.cpp.

References CSeqUtils::CreateSeq_loc(), CRangeCollection< Position >::empty(), CHitMatrixWidget::GetObjectSelection(), CHitMatrixWidget::GetQueryRangeSelection(), CHitMatrixWidget::GetSubjectRangeSelection(), ITERATE, CDotMatrixView::m_AlnWidget, CDotMatrixView::m_DataSource, CProjectViewBase::x_GetScope(), and CProjectViewBase::x_HasProject().

◆ GetSelection() [12/14] ◆ GetSelection() [13/14]

shall return data objects representing selected things, return one data object for every selected thing.

Implementation shall not clear the container as it can be used for accumulating objects.

Reimplemented from CProjectView.

Definition at line 385 of file multi_align_view.cpp.

References CSeqUtils::CreateSeq_loc(), CRangeCollection< Position >::Empty(), CAlnMultiWidget::GetSelectedRows(), ITERATE, CMultiAlignView::m_AlnWidget, CMultiAlignView::m_DataSource, row, CProjectViewBase::x_GetScope(), CMultiAlignView::x_GetSeqRangeSelection(), and CProjectViewBase::x_HasProject().

◆ GetSelection() [14/14]

shall return data objects representing selected things, return one data object for every selected thing.

Implementation shall not clear the container as it can be used for accumulating objects.

Reimplemented from CProjectView.

Definition at line 1102 of file phy_tree_view.cpp.

References CPhyloTree::GetCurrentNodeIdx(), CTreeModel< TNode >::GetNode(), CRef< C, Locker >::GetPointer(), CPhyloTree::GetSelected(), CPhyloTreeDataSource::GetTree(), CPhyTreeView::GetWidget(), CPhyloTree::HasCurrentNode(), ITERATE, CPhyTreeView::m_Cont, CPhyTreeView::m_CurrentNode, CPhyTreeView::m_DataSource, n, CRef< C, Locker >::Reset(), TreeConvert2Container(), CProjectViewBase::x_GetScope(), and CProjectViewBase::x_HasProject().

◆ GetSeq1() ◆ GetSeq2() ◆ GetSeqLocs() [1/2] ◆ GetSeqLocs() [2/2] ◆ GetState() ◆ GetStateLabel() string CNetBlastJobDescriptor::GetStateLabel ( EState  state ) static ◆ GetStatusText() string CBlastSearchTask::GetStatusText ( void  ) const virtual ◆ GetSubject() [1/2] ◆ GetSubject() [2/2] ◆ GetSubjectType()

Definition at line 204 of file blast_search_params.hpp.

Referenced by CBLASTToolManager::CanQuickLaunch(), CBLASTToolManager::GetTask(), CBLASTToolManager::QuickLaunch(), CBLASTSearchOptionsPanel::TransferDataFromWindow(), CBLASTSearchParamsPanel::TransferDataFromWindow(), CBLASTSearchOptionsPanel::TransferDataToWindow(), CBLASTSearchParamsPanel::TransferDataToWindow(), CBLASTSearchOptionsPanel::x_CheckDBLoaded(), CBLASTSeqToolJob::x_CreateProjectItems(), CBLASTSearchParamsPanel::x_HideShowInputs(), CBLASTSearchOptionsPanel::x_UpdateSubjects(), and CBLASTSearchOptionsPanel::x_UpdateSubjectType().

◆ GetSubjSeqLocs() [1/2] ◆ GetSubjSeqLocs() [2/2] ◆ GetSubmitted() bool CNetBlastDMSearchFormPanel::GetSubmitted ( ) const inline ◆ GetSubmitTime() time_t CNetBlastJobDescriptor::GetSubmitTime ( ) const ◆ GetTask() [1/5] IAppTask * CBLASTToolManager::GetTask ( ) virtual

Once parameters are gathered and validated this function is called to produce the final Task object that will be executed to do the actual computational work.

Implements IUIToolManager.

Definition at line 269 of file blast_tool_manager.cpp.

References CBLASTParams::eNCBIDB, CBLASTToolManager::GetBLASTDataSource(), CUIObject::GetLabel(), IServiceLocator::GetServiceByType(), CBLASTParams::GetSubjectType(), CBLASTToolManager::m_Descriptor, CBLASTToolManager::m_Params, CBLASTToolManager::m_ProjectParams, CBLASTToolManager::m_SrvLocator, CBLASTParams::PrintParams(), CRef< C, Locker >::Release(), and SProjectSelectorParams::ToLoadingOptions().

Referenced by CBLASTToolManager::QuickLaunch().

◆ GetTask() [2/5] IAppTask * CCreateGeneModelToolManager::GetTask ( ) virtual ◆ GetTask() [3/5] IAppTask * CNetBLASTUILoadManager::GetTask ( ) virtual

Once parameters are gathered and validated this function is called to produce the final Task object that will be executed to do the actual computational work.

Implements IUIToolManager.

Definition at line 177 of file net_blast_ui_load_manager.cpp.

References CUIObject::GetLabel(), CProjectSelectorPanel::GetParams(), CNetBLASTLoadOptionPanel::GetRIDs(), i, Info(), CBlastSearchTask::Init_RetrieveRID(), LOG_POST, SProjectSelectorParams::m_CreateFolder, CNetBLASTUILoadManager::m_DataSource, CNetBLASTUILoadManager::m_Descriptor, SProjectSelectorParams::m_FolderName, CNetBLASTUILoadManager::m_OptionPanel, CNetBLASTUILoadManager::m_ProjectParams, CNetBLASTUILoadManager::m_ProjectSelPanel, CNetBLASTUILoadManager::m_SrvLocator, CBlastSearchTask::SetLoadingOptions(), and SProjectSelectorParams::ToLoadingOptions().

◆ GetTask() [4/5]

Once parameters are gathered and validated this function is called to produce the final Task object that will be executed to do the actual computational work.

Implements IUIToolManager.

Definition at line 175 of file psl_load_manager.cpp.

◆ GetTask() [5/5] IAppTask * CTextAlignLoaderManager::GetTask ( ) virtual

Once parameters are gathered and validated this function is called to produce the final Task object that will be executed to do the actual computational work.

Implements IUIToolManager.

Definition at line 172 of file text_align_load_manager.cpp.

◆ GetThreshold() long CBLASTSearchParamsPanel::GetThreshold ( ) const inline ◆ GetType() ◆ GetTypeDescriptor() [1/7] ◆ GetTypeDescriptor() [2/7] ◆ GetTypeDescriptor() [3/7] ◆ GetTypeDescriptor() [4/7] ◆ GetTypeDescriptor() [5/7] ◆ GetTypeDescriptor() [6/7] ◆ GetTypeDescriptor() [7/7] ◆ GetVisibleRanges() [1/6] void CAlignSpanView::GetVisibleRanges ( CVisibleRange &  vrange ) const virtual ◆ GetVisibleRanges() [2/6] void CAnnotCompareView::GetVisibleRanges ( CVisibleRange &  vrange ) const virtual

populate a visible range event for broadcasting

Populate a visible range event prior to broadcasting.

Reimplemented from CProjectView.

Definition at line 307 of file annot_compare_view.cpp.

◆ GetVisibleRanges() [3/6] void CCrossAlignView::GetVisibleRanges ( CVisibleRange &  vrange ) const virtual

populate a visible range event for broadcasting

Populate a visible range event prior to broadcasting.

Reimplemented from CProjectView.

Definition at line 305 of file cross_align_view.cpp.

References CVisibleRange::AddLocation(), CGlRect< T >::Bottom(), ERR_POST, Error(), CCrossAlnWidget::GetPort(), CGlPane::GetVisibleRect(), CGlRect< T >::Left(), CCrossAlignView::m_AlnWidget, CCrossAlignView::m_DataSource, CRef< C, Locker >::Reset(), CGlRect< T >::Right(), CSeq_loc::SetId(), CSeq_loc::SetInt(), and CGlRect< T >::Top().

◆ GetVisibleRanges() [4/6] void CDotMatrixView::GetVisibleRanges ( CVisibleRange &  vrange ) const virtual

populate a visible range event for broadcasting

Populate a visible range event prior to broadcasting.

Reimplemented from CProjectView.

Definition at line 311 of file dot_matrix_view.cpp.

References CVisibleRange::AddLocation(), CGlRect< T >::Bottom(), ERR_POST, Error(), CHitMatrixWidget::GetPort(), CGlPane::GetVisibleRect(), CRef< C, Locker >::IsNull(), CGlRect< T >::Left(), CDotMatrixView::m_AlnWidget, CDotMatrixView::m_DataSource, CRef< C, Locker >::Reset(), CGlRect< T >::Right(), CSeq_loc::SetId(), CSeq_loc::SetInt(), and CGlRect< T >::Top().

◆ GetVisibleRanges() [5/6] void CMPCrossAlignView::GetVisibleRanges ( CVisibleRange &  vrange ) const virtual

populate a visible range event for broadcasting

Populate a visible range event prior to broadcasting.

Reimplemented from CProjectView.

Definition at line 368 of file mp_cross_align_view.cpp.

◆ GetVisibleRanges() [6/6] void CPhyTreeView::GetVisibleRanges ( CVisibleRange &  vrange ) const virtual

populate a visible range event for broadcasting

Populate a visible range event prior to broadcasting.

Reimplemented from CProjectView.

Definition at line 1433 of file phy_tree_view.cpp.

◆ GetWaitPeriod() CTimeSpan CNetBlastMonitoringJob::GetWaitPeriod ( ) virtual ◆ GetWidget() [1/2]

Definition at line 816 of file phy_tree_view.cpp.

References CPhyTreeView::kPhylpWidgetID, and CPhyTreeView::m_Panel.

Referenced by CChangePhyloPropertyCmd::CChangePhyloPropertyCmd(), CPhyTreeView::GetSelection(), CPhyTreeView::InitView(), CPhyTreeView::LoadSettings(), CPhyTreeView::OnBioTreeChanged(), CPhyTreeView::OnCreateSelectedSubtree(), CPhyTreeView::OnExportTree(), CPhyTreeView::OnProjectChanged(), CPhyTreeView::OnSomethingEdited(), CChangePhyloPropertyCmd::PerformEdit(), CPhyTreeView::SaveSettings(), CPhyTreeView::SetRegistryPath(), and CPhyTreeView::x_OnSetSelection().

◆ GetWidget() [2/2] wxSizer * CNetBLAST_DMSearchForm::GetWidget ( wxWindow *  ) virtual ◆ GetWindow() [1/7] wxWindow * CAlignSpanView::GetWindow ( ) virtual ◆ GetWindow() [2/7] wxWindow * CAnnotCompareView::GetWindow ( ) virtual ◆ GetWindow() [3/7] wxWindow * CCrossAlignView::GetWindow ( ) virtual ◆ GetWindow() [4/7] wxWindow * CDotMatrixView::GetWindow ( ) virtual ◆ GetWindow() [5/7] wxWindow * CMPCrossAlignView::GetWindow ( ) virtual ◆ GetWindow() [6/7] wxWindow * CMultiAlignView::GetWindow ( ) virtual ◆ GetWindow() [7/7] wxWindow * CPhyTreeView::GetWindow ( ) virtual ◆ GetWmDir() ◆ GetWMDir() string CNGAlignParams::GetWMDir ( ) const inline ◆ GetWMTaxId() int CNGAlignParams::GetWMTaxId ( ) const inline ◆ GetWordSize() [1/2] long CBLASTSearchParamsPanel::GetWordSize ( ) const inline ◆ GetWordSize() [2/2] long CNGAlignParams::GetWordSize ( ) const inline ◆ HasErrors() bool CNetBlastLoadingJob::HasErrors ( ) const ◆ Id() [1/2] ◆ Id() [2/2] ◆ Init() [1/32] void CBLAST_DB_Dialog::Init ( void  ) ◆ Init() [2/32] void CBLASTSearchOptionsPanel::Init ( void  )

Definition at line 166 of file blast_search_options_panel.cpp.

References CBLASTDatabases::eInitial, CBLASTSearchOptionsPanel::m_BrowseDBBtn, CBLASTSearchOptionsPanel::m_DatabaseCombo, CBLASTSearchOptionsPanel::m_DataSource, CBLASTSearchOptionsPanel::m_DBLoadState, CBLASTSearchOptionsPanel::m_DBSizer, CBLASTSearchOptionsPanel::m_LocalDBCtrl, CBLASTSearchOptionsPanel::m_LocalDBLoaderCtrl, CBLASTSearchOptionsPanel::m_LocalDBSizer, CBLASTSearchOptionsPanel::m_LocalSeqsSizer, CBLASTSearchOptionsPanel::m_LocalSizer, CBLASTSearchOptionsPanel::m_NCBIDBSizer, CBLASTSearchOptionsPanel::m_NucObjects, CBLASTSearchOptionsPanel::m_NucRadio, CBLASTSearchOptionsPanel::m_Params, CBLASTSearchOptionsPanel::m_ProgramCombo, CBLASTSearchOptionsPanel::m_ProtObjects, CBLASTSearchOptionsPanel::m_ProtRadio, CBLASTSearchOptionsPanel::m_QueryCombo, CBLASTSearchOptionsPanel::m_QueryListCtrl, CBLASTSearchOptionsPanel::m_QuerySeqSetCombo, CBLASTSearchOptionsPanel::m_QuerySeqSetStatic, CBLASTSearchOptionsPanel::m_SubjectListCtrl, CBLASTSearchOptionsPanel::m_SubjectSeqSetCombo, CBLASTSearchOptionsPanel::m_SubjectSeqSetStatic, CBLASTSearchOptionsPanel::m_SubjectTypeLDBCtrl, CBLASTSearchOptionsPanel::m_SubjectTypeNCBICtrl, CBLASTSearchOptionsPanel::m_SubjectTypeSeqsCtrl, CBLASTSearchOptionsPanel::m_ToolName, and NULL.

Referenced by CBLASTSearchOptionsPanel::CBLASTSearchOptionsPanel().

◆ Init() [3/32] void CBLASTSearchParamsPanel::Init ( void  )

Definition at line 126 of file blast_search_params_panel.cpp.

References CBLASTSearchParamsPanel::m_chbStandalone, CBLASTSearchParamsPanel::m_CompartCheck, CBLASTSearchParamsPanel::m_DbGenCodeCombo, CBLASTSearchParamsPanel::m_DbGenCodeLabel, CBLASTSearchParamsPanel::m_GeneralSizer, CBLASTSearchParamsPanel::m_LCRegionsCheck, CBLASTSearchParamsPanel::m_Params, CBLASTSearchParamsPanel::m_QueryGenCodeCombo, CBLASTSearchParamsPanel::m_QueryGenCodeLabel, CBLASTSearchParamsPanel::m_RepeatsCheck, CBLASTSearchParamsPanel::m_RepeatType, CBLASTSearchParamsPanel::m_ThreshInput, CBLASTSearchParamsPanel::m_ThreshLabel, CBLASTSearchParamsPanel::m_WMDownload, CBLASTSearchParamsPanel::m_WMStatic, CBLASTSearchParamsPanel::m_WMStaticBoxSizer, CBLASTSearchParamsPanel::m_WMTaxIds, and NULL.

Referenced by CBLASTSearchParamsPanel::CBLASTSearchParamsPanel().

◆ Init() [4/32] void SCleanupAlignmentsParams::Init ( void  ) ◆ Init() [5/32] void CCleanupAlignmentsParamsPanel::Init ( void  ) ◆ Init() [6/32] void CClustalOmegaToolParams::Init ( void  ) ◆ Init() [7/32] void CClustalwToolParams::Init ( void  ) ◆ Init() [8/32] void CFindOverlapPanel::Init ( void  ) ◆ Init() [9/32] void CFindOverlapParams::Init ( void  ) ◆ Init() [10/32] void SGroupAlignmentsParams::Init ( void  )

Definition at line 67 of file group_alignments_params_panel.cpp.

References SGroupAlignmentsParams::m_GroupByEST, SGroupAlignmentsParams::m_GroupByGenBank, SGroupAlignmentsParams::m_GroupByHTGS, SGroupAlignmentsParams::m_GroupByLikeTaxId, SGroupAlignmentsParams::m_GroupByPatent, SGroupAlignmentsParams::m_GroupByPredictedRefSeq, SGroupAlignmentsParams::m_GroupByRefSeq, SGroupAlignmentsParams::m_GroupBySeqId, SGroupAlignmentsParams::m_GroupByStrand, SGroupAlignmentsParams::m_GroupByTaxId, and SGroupAlignmentsParams::m_GroupByWGS.

Referenced by CGroupAlignmentsParamsPanel::RestoreDefaults().

◆ Init() [11/32] void CGroupAlignmentsParamsPanel::Init ( void  )

Definition at line 175 of file group_alignments_params_panel.cpp.

References CGroupAlignmentsParamsPanel::m_GroupByEST, CGroupAlignmentsParamsPanel::m_GroupByGenBank, CGroupAlignmentsParamsPanel::m_GroupByHTGS, CGroupAlignmentsParamsPanel::m_GroupByLikeTaxId, CGroupAlignmentsParamsPanel::m_GroupByPatent, CGroupAlignmentsParamsPanel::m_GroupByPredictedRefSeq, CGroupAlignmentsParamsPanel::m_GroupByRefSeq, CGroupAlignmentsParamsPanel::m_GroupBySeqId, CGroupAlignmentsParamsPanel::m_GroupByStrand, CGroupAlignmentsParamsPanel::m_GroupByTaxId, CGroupAlignmentsParamsPanel::m_GroupByWGS, CGroupAlignmentsParamsPanel::m_InputListDirty, CGroupAlignmentsParamsPanel::m_InputObjects, CGroupAlignmentsParamsPanel::m_ObjectList, CGroupAlignmentsParamsPanel::m_Params, and NULL.

Referenced by CGroupAlignmentsParamsPanel::CGroupAlignmentsParamsPanel().

◆ Init() [12/32] void CKalignToolParams::Init ( void  ) ◆ Init() [13/32] void CMafftToolParams::Init ( void  ) ◆ Init() [14/32] void SMergeAlignmentsParams::Init ( void  ) ◆ Init() [15/32] void CMergeAlignmentsParamsPanel::Init ( void  ) ◆ Init() [16/32] void CMuscleToolParams::Init ( void  ) ◆ Init() [17/32] void CNeedlemanWunschToolParams::Init ( void  ) ◆ Init() [18/32] void CNetBlastDMSearchFormPanel::Init ( void  ) ◆ Init() [19/32] void CNetBLAST_DMSearchForm::Init ( void  ) virtual ◆ Init() [20/32] void CNetBLASTLoadOptionPanel::Init ( void  ) ◆ Init() [21/32] void CNGAlignParams::Init ( void  ) ◆ Init() [22/32] void CSplignPanel::Init ( void  ) ◆ Init() [23/32] void CSplignParams::Init ( void  ) ◆ Init() [24/32] void CTaxTreeToolParams::Init ( void  ) ◆ Init() [25/32] void CTreeBuilderPanel::Init ( void  ) ◆ Init() [26/32] void CTreeBuilderParams::Init ( void  ) ◆ Init() [27/32] void CTextAlignObjectLoader::Init ( void  ) ◆ Init() [28/32] void CMuscleToolPanel::Init ( void  ) ◆ Init() [29/32] void CNGAlignPanel::Init ( void  ) ◆ Init() [30/32] void CTaxTreeToolPanel::Init ( void  ) ◆ Init() [31/32]

Definition at line 208 of file net_blast_job_descr.cpp.

References _ASSERT, CNetBlastJobDescriptor::eInitial, CNetBlastJobDescriptor::eInvalidState, db_map_base< K, T >::end(), eq(), eUnknown, db_map_base< K, T >::find(), CBLASTParams::GetCurrDatabase(), CBLASTDatabases::GetDbMap(), CBLASTParams::GetEntrezQuery(), CBLASTDatabases::GetInstance(), CBLASTParams::GetJobTitle(), CBLASTParams::IsSubjNucInput(), CBLASTDatabases::Loaded(), CNetBlastJobDescriptor::m_JobTitle, CNetBlastJobDescriptor::m_Mutex, CNetBlastJobDescriptor::m_NetBlastDS, CNetBlastJobDescriptor::m_RemoteBlast, CNetBlastJobDescriptor::m_RID, CNetBlastJobDescriptor::m_State, msg(), NCBI_THROW, CRef< C, Locker >::Reset(), and CBLASTParams::ToBlastOptions().

◆ Init() [32/32] ◆ Init_Monitoring() void CBlastSearchTask::Init_Monitoring ( TDescriptors &  descriptors ) virtual ◆ Init_RetrieveRID() void CBlastSearchTask::Init_RetrieveRID ( const vector< string > &  RIDs ) virtual

setup the task for retrieving results

Definition at line 101 of file blast_search_task.cpp.

References CBlastSearchTask::eMonitor, CBlastSearchTask::eRetrieve, CGBProjectHandle::GetScope(), IServiceLocator::GetServiceByType(), CSelectProjectOptions::GetTargetProjectId(), CBlastSearchTask::m_Command, CBlastSearchTask::m_CurrTask, CAppTask::m_Descr, CBlastSearchTask::m_LoadingJob, CBlastSearchTask::m_LoadingOptions, CBlastSearchTask::m_NetBlastDS, CBlastSearchTask::m_SrvLocator, CBlastSearchTask::m_Stage, CBlastSearchTask::m_ToolName, n, NStr::NumericToString(), and CRef< C, Locker >::Reset().

Referenced by CNetBLASTUILoadManager::GetTask().

◆ Init_SubmitSearch()

setup the task for submitting and monitoring BLAST jobs, and for retrieving results

Definition at line 63 of file blast_search_task.cpp.

References CBlastSearchTask::eSubmit, CBLASTParams::GetJobTitle(), CBLASTParams::GetSeqLocs(), CBlastSearchTask::m_Command, CBlastSearchTask::m_CurrTask, CAppTask::m_Descr, CBlastSearchTask::m_NetBlastDS, CBlastSearchTask::m_Stage, CBlastSearchTask::m_SubmittingJob, CBlastSearchTask::m_ToolName, n, NStr::NumericToString(), CRef< C, Locker >::Reset(), and CAppJobTask::SetReportErrors().

◆ InitUI() [1/21] void CBLASTToolManager::InitUI ( ) virtual ◆ InitUI() [2/21] void CCleanupAlignmentsToolManager::InitUI ( ) virtual ◆ InitUI() [3/21] void CClustalOmegaTool::InitUI ( ) virtual ◆ InitUI() [4/21] void CClustalwTool::InitUI ( ) virtual ◆ InitUI() [5/21] void CCreateGeneModelToolManager::InitUI ( ) virtual ◆ InitUI() [6/21] void CFindOverlapTool::InitUI ( ) virtual ◆ InitUI() [7/21] void CGroupAlignmentsToolManager::InitUI ( ) virtual ◆ InitUI() [8/21] void CKalignTool::InitUI ( ) virtual ◆ InitUI() [9/21] void CMafftTool::InitUI ( ) virtual ◆ InitUI() [10/21] void CMergeAlignmentsToolManager::InitUI ( ) virtual ◆ InitUI() [11/21] void CMuscleTool::InitUI ( ) virtual ◆ InitUI() [12/21] void CNetBLASTUILoadManager::InitUI ( ) virtual ◆ InitUI() [13/21] void CNGAlignTool::InitUI ( ) virtual ◆ InitUI() [14/21] void CProSplignTool::InitUI ( ) virtual ◆ InitUI() [15/21] void CSplignTool::InitUI ( ) virtual ◆ InitUI() [16/21] void CCommonTaxTreeTool::InitUI ( ) virtual ◆ InitUI() [17/21] void CTreeBuilderTool::InitUI ( ) virtual ◆ InitUI() [18/21] void CAdvancedCleanupTool::InitUI ( ) virtual ◆ InitUI() [19/21] void CCreateNeedlemanWunschToolManager::InitUI ( ) virtual ◆ InitUI() [20/21] void CPslLoadManager::InitUI ( ) virtual ◆ InitUI() [21/21] void CTextAlignLoaderManager::InitUI ( ) virtual ◆ InitView() [1/3]

initialize view with data, inside this function the view must call CProjectService::AttachView to connect to a project

Reimplemented from CProjectView.

Definition at line 135 of file mp_cross_align_view.cpp.

References _ASSERT, IWindowManagerService::ActivateClient(), IViewManagerService::CreateViewInstance(), CProjectViewBase::CreateViewWindow(), CSeq_id_Handle::GetHandle(), IServiceLocator::GetServiceByType(), IWorkbench::GetViewManagerService(), CMPCrossAlignView::GetWindow(), CProjectViewBase::GetWindow(), IWorkbench::GetWindowManagerService(), i, CMPCrossAlignView::m_MainSplitter, CMPCrossAlignView::m_OrigAlign, CMPCrossAlignView::m_OrigAnnot, CMPCrossAlignView::m_Views, CProjectViewBase::m_Workbench, IWindowManagerService::RegisterActiveClient(), CConstRef< C, Locker >::Reset(), CProjectView::SetVisibleRangeService(), IWindowManagerService::UnRegisterActiveClient(), wxID_ANY, CProjectViewBase::x_AttachToProject(), CProjectViewBase::x_ReportInvalidInputData(), and CProjectViewBase::x_UpdateContentLabel().

◆ InitView() [2/3] ◆ InitView() [3/3]

initialize view with data, inside this function the view must call CProjectService::AttachView to connect to a project

Reimplemented from CProjectView.

Definition at line 839 of file phy_tree_view.cpp.

References _ASSERT, CProjectViewEvent::eData, Error(), CUser_field_Base::C_Data::GetBool(), CUser_field_Base::GetData(), CUser_object::GetField(), CUser_field_Base::C_Data::GetInt(), CPhyloTreeScheme::GetLayoutIdx(), CException::GetMsg(), CPhyloTreeWidget::GetScheme(), IServiceLocator::GetServiceByType(), CPhyTreeView::GetWidget(), CUser_object::HasField(), CPhyloTreeWidget::HasScheme(), CUser_field_Base::C_Data::IsBool(), CUser_field_Base::C_Data::IsInt(), ITERATE, CPhyloTreeWidget::LoadSettings(), LOG_POST, CPhyTreeView::m_BioTreeContainer, CPhyTreeView::m_InitialLayout, CPhyTreeView::m_InitialRotateLabels, CPhyTreeView::m_InitialUseDistances, CProjectViewBase::m_Workbench, CProjectViewBase::OnProjectChanged(), CConstRef< C, Locker >::Reset(), CProjectViewBase::x_AttachToProject(), and CProjectViewBase::x_ReportInvalidInputData().

◆ IsCompartmentsRequested() bool CBLASTParams::IsCompartmentsRequested ( ) const inline ◆ IsCompatible() ◆ IsCompatibleWith() [1/2] bool CMPCrossAlignViewFactory::IsCompatibleWith ( const CObject &  object, objects::CScope &  scope  ) virtual ◆ IsCompatibleWith() [2/2] bool CMultiAlignViewFactory::IsCompatibleWith ( const CObject &  object, objects::CScope &  scope  ) virtual ◆ IsCompletedState() [1/4] bool CBLASTToolManager::IsCompletedState ( ) virtual ◆ IsCompletedState() [2/4] bool CNetBLASTUILoadManager::IsCompletedState ( ) virtual ◆ IsCompletedState() [3/4] bool CPslLoadManager::IsCompletedState ( ) virtual ◆ IsCompletedState() [4/4] bool CTextAlignLoaderManager::IsCompletedState ( ) virtual ◆ IsDatabase() bool CBLAST_Dlg_Item::IsDatabase ( ) const inline ◆ IsDeleted() bool CNetBlastJobDescriptor::IsDeleted ( ) const ◆ IsExpanded() bool CBLAST_Dlg_Item::IsExpanded ( ) const inline ◆ IsFinalState() [1/5] bool CBLASTToolManager::IsFinalState ( ) virtual ◆ IsFinalState() [2/5] bool CNetBLASTUILoadManager::IsFinalState ( ) virtual ◆ IsFinalState() [3/5] bool CNGAlignTool::IsFinalState ( ) virtual ◆ IsFinalState() [4/5] bool CPslLoadManager::IsFinalState ( ) virtual ◆ IsFinalState() [5/5] bool CTextAlignLoaderManager::IsFinalState ( ) virtual ◆ IsInitialState() [1/2] bool CPslLoadManager::IsInitialState ( ) virtual ◆ IsInitialState() [2/2] bool CTextAlignLoaderManager::IsInitialState ( ) virtual ◆ IsInputValid() bool CNetBLASTLoadOptionPanel::IsInputValid ( ) ◆ IsMultiScopeInputAccepted() virtual bool CNGAlignTool::IsMultiScopeInputAccepted ( ) const inlineprotectedvirtual

Definition at line 82 of file ngalign_tool.hpp.

◆ IsNucDatabase() ◆ IsNucInput() [1/3] bool & CBLASTParams::IsNucInput ( )

Definition at line 275 of file blast_search_params.cpp.

References CBLASTParams::m_NucInput.

Referenced by CBLASTToolManager::QuickLaunch(), CBLASTToolManager::SaveSettings(), CBLASTParams::ToArgVec(), CBLASTSearchOptionsPanel::TransferDataFromWindow(), CBLASTSearchOptionsPanel::TransferDataToWindow(), CBLASTSearchParamsPanel::TransferDataToWindow(), CBLASTToolManager::x_CreateOptionsPanelIfNeeded(), CBLASTSeqToolJob::x_CreateProjectItems(), CBLASTSearchOptionsPanel::x_FillQueryList(), CBLASTSearchParamsPanel::x_HideShowInputs(), CBLASTSearchOptionsPanel::x_OnInputTypeChanged(), and CBLASTSearchOptionsPanel::x_UpdateQuerySeqSet().

◆ IsNucInput() [2/3] bool CBLASTParams::IsNucInput ( ) const ◆ IsNucInput() [3/3] ◆ IsOpen() bool CNetBLASTUIDataSource::IsOpen ( ) virtual ◆ IsStandaloneRequested() bool CBLASTParams::IsStandaloneRequested ( ) const inline ◆ IsSubjNucInput() bool CBLASTParams::IsSubjNucInput ( ) const ◆ IsVisible() bool CBLAST_Dlg_Item::IsVisible ( void  ) const inline ◆ Label() [1/2] ◆ Label() [2/2] ◆ LoadFromStream()

Definition at line 136 of file text_align_object_loader.cpp.

References _ASSERT, _DEBUG_ARG, _TRACE, CMessageListenerBase::Count(), CAlnReader::eAlpha_Nucleotide, CAlnReader::eAlpha_Protein, CLabel::eDefault, CTextAlignParams::GetBegin(), CTextAlignParams::GetEnd(), CMessageListenerBase::GetError(), CTextAlnReader::GetFilteredSeqEntry(), CLabel::GetLabel(), CTextAlignParams::GetMatch(), CTextAlignParams::GetMiddle(), CTextAlignParams::GetSeqType(), ILineError::GetText(), CTextAlignParams::GetUnknown(), i, NStr::IsBlank(), label, CTextAlignObjectLoader::m_Params, CTextAlignObjectLoader::m_Scope, CAlnReader::Read(), CAlnReader::SetAlphabet(), CAlnReader::SetBeginningGap(), CSeq_annot_Base::SetData(), CAlnReader::SetEndGap(), CAlnReader::SetMatch(), CAlnReader::SetMiddleGap(), CAlnReader::SetMissing(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), and ToStdString().

Referenced by CTextAlignObjectLoader::Execute().

◆ LoadSettings() [1/33] void CAlignSpanView::LoadSettings ( ) virtual ◆ LoadSettings() [2/33] void CBLASTSearchOptionsPanel::LoadSettings ( ) virtual ◆ LoadSettings() [3/33] virtual void CBLASTSearchParamsPanel::LoadSettings ( ) inlinevirtual ◆ LoadSettings() [4/33] void CBLASTToolManager::LoadSettings ( ) virtual

Implements IRegSettings.

Definition at line 569 of file blast_tool_manager.cpp.

References CBLASTParams::FromUserObject(), CRegistryReadView::GetBool(), CRegistryReadView::GetField(), CGuiRegistry::GetInstance(), CConstRef< C, Locker >::GetObject(), CGuiRegistry::GetReadView(), CGuiRegistry::GetString(), CRegistryReadView::HasField(), ncbi::grid::netcache::search::fields::key, kLocalWinMaskDirPath, kParamsTag, kUseNucForMixInput, CBLASTToolManager::m_LocalWinMaskDirPath, CBLASTToolManager::m_Params, CBLASTToolManager::m_RegPath, CBLASTToolManager::m_UseNucForMixInput, and CGuiRegistryUtil::MakeKey().

◆ LoadSettings() [5/33] void SCleanupAlignmentsParams::LoadSettings ( ) virtual ◆ LoadSettings() [6/33] void CCleanupAlignmentsParamsPanel::LoadSettings ( ) virtual ◆ LoadSettings() [7/33] void CClustalOmegaToolParams::LoadSettings ( ) virtual

Implements IRegSettings.

Definition at line 114 of file clustal_omega_tool_params.cpp.

References FnToWxString(), CRegistryReadView::GetBool(), CGuiRegistry::GetInstance(), CGuiRegistry::GetReadView(), CRegistryReadView::GetString(), CGuiRegistry::GetString(), kClustalwPath, kCommandLine, kGenerateTree, CClustalOmegaToolParams::m_ClustalOmegaPath, CClustalOmegaToolParams::m_CommandLine, CClustalOmegaToolParams::m_GenerateTree, CClustalOmegaToolParams::m_RegPath, ToStdString(), and ToWxString().

◆ LoadSettings() [8/33] void CClustalwToolParams::LoadSettings ( ) virtual

Implements IRegSettings.

Definition at line 104 of file clustalw_tool_params.cpp.

References FnToWxString(), CRegistryReadView::GetBool(), CGuiRegistry::GetInstance(), CGuiRegistry::GetReadView(), CRegistryReadView::GetString(), CGuiRegistry::GetString(), kClustalwPath, kCommandLine, kGenerateTree, CClustalwToolParams::m_ClustalWPath, CClustalwToolParams::m_CommandLine, CClustalwToolParams::m_GenerateTree, CClustalwToolParams::m_RegPath, ToStdString(), and ToWxString().

◆ LoadSettings() [9/33] void CFindOverlapPanel::LoadSettings ( ) virtual ◆ LoadSettings() [10/33] void CFindOverlapParams::LoadSettings ( ) virtual

Implements IRegSettings.

Definition at line 101 of file find_overlap_params.cpp.

References CGuiRegistry::GetInstance(), CRegistryReadView::GetInt(), CGuiRegistry::GetReadView(), CRegistryReadView::GetString(), kBlastParamsTag, kFilterTag, kMaxSlopTag, CFindOverlapParams::m_BlastParams, CFindOverlapParams::m_FilterQty, CFindOverlapParams::m_MaxSlop, CFindOverlapParams::m_RegPath, ToStdString(), and ToWxString().

◆ LoadSettings() [11/33] void SGroupAlignmentsParams::LoadSettings ( ) virtual

Implements IRegSettings.

Definition at line 118 of file group_alignments_params_panel.cpp.

References CRegistryReadView::GetBool(), CGuiRegistry::GetInstance(), CGuiRegistry::GetReadView(), kGroupByEST, kGroupByHTGS, kGroupByLikeTaxId, kGroupByPatent, kGroupByPredictedRefSeq, kGroupByRefSeq, kGroupBySeqId, kGroupByTaxId, kGroupByWGS, SGroupAlignmentsParams::m_GroupByEST, SGroupAlignmentsParams::m_GroupByHTGS, SGroupAlignmentsParams::m_GroupByLikeTaxId, SGroupAlignmentsParams::m_GroupByPatent, SGroupAlignmentsParams::m_GroupByPredictedRefSeq, SGroupAlignmentsParams::m_GroupByRefSeq, SGroupAlignmentsParams::m_GroupBySeqId, SGroupAlignmentsParams::m_GroupByTaxId, SGroupAlignmentsParams::m_GroupByWGS, and SGroupAlignmentsParams::m_RegPath.

◆ LoadSettings() [12/33] void CGroupAlignmentsParamsPanel::LoadSettings ( ) virtual ◆ LoadSettings() [13/33] void CKalignToolParams::LoadSettings ( ) virtual

Implements IRegSettings.

Definition at line 110 of file kalign_tool_params.cpp.

References CRegistryReadView::GetBool(), CGuiRegistry::GetInstance(), CGuiRegistry::GetReadView(), CRegistryReadView::GetString(), CGuiRegistry::GetString(), kAlignPath, kCommandLine, kQuietMode, CKalignToolParams::m_CommandLine, CKalignToolParams::m_KalignPath, CKalignToolParams::m_QuietFlag, CKalignToolParams::m_RegPath, ToStdString(), and ToWxString().

◆ LoadSettings() [14/33] void CMafftToolParams::LoadSettings ( ) virtual

Implements IRegSettings.

Definition at line 115 of file mafft_tool_params.cpp.

References CRegistryReadView::GetBool(), CGuiRegistry::GetInstance(), CGuiRegistry::GetReadView(), CRegistryReadView::GetString(), CGuiRegistry::GetString(), kAutoFlag, kCommandLine, kMafftPath, kQuietMode, CMafftToolParams::m_AutoFlag, CMafftToolParams::m_CommandLine, CMafftToolParams::m_MafftPath, CMafftToolParams::m_QuietFlag, CMafftToolParams::m_RegPath, ToStdString(), and ToWxString().

◆ LoadSettings() [15/33] void SMergeAlignmentsParams::LoadSettings ( ) virtual

Implements IRegSettings.

Definition at line 93 of file merge_alignments_params_panel.cpp.

References CRegistryReadView::GetBool(), CGuiRegistry::GetInstance(), CRegistryReadView::GetInt(), CGuiRegistry::GetReadView(), kDirectionTag, kFillUnalignedTag, kMergeAlgoTag, kMergeFlagsTag, SMergeAlignmentsParams::m_Direction, SMergeAlignmentsParams::m_FillUnaligned, SMergeAlignmentsParams::m_MergeAlgo, SMergeAlignmentsParams::m_MergeFlags, and SMergeAlignmentsParams::m_RegPath.

◆ LoadSettings() [16/33] void CMergeAlignmentsParamsPanel::LoadSettings ( ) virtual ◆ LoadSettings() [17/33] void CMultiAlignView::LoadSettings ( ) virtual ◆ LoadSettings() [18/33] void CMuscleToolParams::LoadSettings ( ) virtual

Implements IRegSettings.

Definition at line 115 of file muscle_tool_params.cpp.

References CRegistryReadView::GetBool(), CGuiRegistry::GetInstance(), CRegistryReadView::GetInt(), CGuiRegistry::GetReadView(), CRegistryReadView::GetString(), CGuiRegistry::GetString(), kCommandLine, kGenerateTree, kMusclePath, kScoringMethod, CMuscleToolParams::m_CommandLine, CMuscleToolParams::m_GenerateTree, CMuscleToolParams::m_MusclePath, CMuscleToolParams::m_RegPath, CMuscleToolParams::m_ScoringMethod, ToStdString(), and ToWxString().

◆ LoadSettings() [19/33] void CNeedlemanWunschToolParams::LoadSettings ( ) virtual

Implements IRegSettings.

Definition at line 120 of file needlemanwunsch_tool_params.cpp.

References CGuiRegistry::GetInstance(), CRegistryReadView::GetInt(), CGuiRegistry::GetReadView(), kBandSize, kFirstSeqFreeEnds, kGapExtendCost, kGapOpenCost, kMatchCost, kMismatchCost, kSecondSeqFreeEnds, CNeedlemanWunschToolParams::m_BandSize, CNeedlemanWunschToolParams::m_FirstSeqFreeEnds, CNeedlemanWunschToolParams::m_GapExtendCost, CNeedlemanWunschToolParams::m_GapOpenCost, CNeedlemanWunschToolParams::m_MatchCost, CNeedlemanWunschToolParams::m_MismatchCost, CNeedlemanWunschToolParams::m_RegPath, and CNeedlemanWunschToolParams::m_SecondSeqFreeEnds.

◆ LoadSettings() [20/33] void CNetBLASTUIDataSource::LoadSettings ( ) virtual ◆ LoadSettings() [21/33] void CNetBLASTUILoadManager::LoadSettings ( ) virtual ◆ LoadSettings() [22/33] void CNGAlignParams::LoadSettings ( ) virtual

Implements IRegSettings.

Definition at line 131 of file ngalign_params.cpp.

References CRegistryReadView::GetBool(), CGuiRegistry::GetInstance(), CRegistryReadView::GetInt(), CGuiRegistry::GetReadView(), CRegistryReadView::GetReal(), CRegistryReadView::GetString(), kAdvParams, kBestHit, keValue, kFilterMode, kJobTitle, kWM_TaxId, kWordSize, CNGAlignParams::m_AdvParams, CNGAlignParams::m_BestHit, CNGAlignParams::m_eValue, CNGAlignParams::m_FilterMode, CNGAlignParams::m_JobTitle, CNGAlignParams::m_RegPath, CNGAlignParams::m_WM_TaxId, CNGAlignParams::m_WordSize, ToStdString(), and ToWxString().

◆ LoadSettings() [23/33] void CPhyTreeView::LoadSettings ( ) virtual ◆ LoadSettings() [24/33] void CSplignPanel::LoadSettings ( ) virtual ◆ LoadSettings() [25/33] void CSplignParams::LoadSettings ( ) virtual

Implements IRegSettings.

Definition at line 130 of file splign_params.cpp.

References CRegistryReadView::GetBool(), CGuiRegistry::GetInstance(), CRegistryReadView::GetInt(), CGuiRegistry::GetReadView(), CRegistryReadView::GetReal(), kcDNA_strandTag, kCompPenaltyTag, kDiscType, kEndGapDetectTag, kMaxGenomicExtentTag, kMaxIntron, kMinCompIdentityTag, kMinExonIdentityTag, kPolyADetectTag, CSplignParams::m_cDNA_strand, CSplignParams::m_CompPenalty, CSplignParams::m_DiscType, CSplignParams::m_EndGapDetect, CSplignParams::m_MaxGenomicExtent, CSplignParams::m_MaxIntron, CSplignParams::m_MinCompIdentity, CSplignParams::m_MinExonIdentity, CSplignParams::m_PolyADetect, and CSplignParams::m_RegPath.

◆ LoadSettings() [26/33] void CTaxTreeToolParams::LoadSettings ( ) virtual ◆ LoadSettings() [27/33] void CTreeBuilderPanel::LoadSettings ( ) virtual ◆ LoadSettings() [28/33] void CTreeBuilderParams::LoadSettings ( ) virtual

Implements IRegSettings.

Definition at line 98 of file tree_builder_params.cpp.

References CGuiRegistry::GetInstance(), CGuiRegistry::GetReadView(), CRegistryReadView::GetString(), kConsTag, kDistTag, kLeafTag, CTreeBuilderParams::m_ConstructMethod, CTreeBuilderParams::m_DistanceMethod, CTreeBuilderParams::m_LeafLabels, CTreeBuilderParams::m_RegPath, and ToWxString().

◆ LoadSettings() [29/33] void CMuscleToolPanel::LoadSettings ( ) virtual ◆ LoadSettings() [30/33] void CNGAlignPanel::LoadSettings ( ) virtual ◆ LoadSettings() [31/33] void CPslLoadManager::LoadSettings ( ) virtual ◆ LoadSettings() [32/33] void CTaxTreeToolPanel::LoadSettings ( ) virtual ◆ LoadSettings() [33/33] void CTextAlignLoaderManager::LoadSettings ( ) virtual ◆ LogDump() void CNGAlignParams::LogDump ( )

Definition at line 147 of file ngalign_params.cpp.

References CSeq_id::eContent, CSeq_id::GetLabel(), CConstRef< C, Locker >::GetPointer(), Info(), LOG_POST, CNGAlignParams::m_AdvParams, CNGAlignParams::m_BestHit, CNGAlignParams::m_eValue, CNGAlignParams::m_FilterMode, CNGAlignParams::m_Queries, CNGAlignParams::m_Subject, CNGAlignParams::m_WM_TaxId, CNGAlignParams::m_WordSize, NON_CONST_ITERATE, NULL, and SConstScopedObject::object.

Referenced by CNGAlignJob::x_CreateProjectItems().

◆ MarkDeleted() void CNetBlastJobDescriptor::MarkDeleted ( bool  deleted ) ◆ NeedsDbGeneticCode() ◆ NeedsQueryGeneticCode() ◆ NeedsThreshold() ◆ OnAlnWidgetSelChanged() void CMultiAlignView::OnAlnWidgetSelChanged ( CEvent *  evt ) ◆ OnBioTreeChanged() void CPhyTreeView::OnBioTreeChanged ( )

Definition at line 967 of file phy_tree_view.cpp.

References _ASSERT, CPhyloTreeDataSource::Clear(), CPhyloTreeScheme::eFancyLabels, CPhyloTreeScheme::eLabelsForLeavesOnly, CPhyloTreeScheme::eLabelsVisible, CStopWatch::Elapsed(), CRef< C, Locker >::Empty(), CPhyloTreeDataSource::GenerateTooltipFormat(), CUser_field_Base::GetData(), CPhyloTreeWidget::GetDS(), CPhyloTree::GetFeatureDict(), CUser_object::GetField(), CPhyloTreeWidget::GetScheme(), CUser_field_Base::C_Data::GetStr(), CPhyloTreeDataSource::GetTree(), CPhyTreeView::GetWidget(), CBioTreeFeatureDictionary::HasFeature(), CUser_object::HasField(), CPhyloTreeWidget::HasScheme(), CPhyloTreeDataSource::Init(), CRef< C, Locker >::IsNull(), CUser_field_Base::C_Data::IsStr(), CPhyloTreeScheme::LoadCurrentSettings(), CPhyTreeView::m_BioTreeContainer, CPhyTreeView::m_DataSource, m_DataSourceInitTimer, CPhyTreeView::m_InitialLayout, CPhyTreeView::m_InitialRotateLabels, CPhyTreeView::m_InitialUseDistances, CPhyTreeView::m_Scheme, NULL, CPhyTreeView::RebuildObjectIndex(), CPhyloTreeWidget::RedrawDataSource(), CPhyloTreeDataSource::Relabel(), CPhyloTreeWidget::RemoveCurrentDataSource(), CRef< C, Locker >::Reset(), CPhyloTreeWidget::SetCurrRenderer(), CPhyloTreeWidget::SetDataSourceNoUpdate(), CPhyloTreeScheme::SetLabelFormat(), CPhyloTreeScheme::SetLabelStyle(), CPhyloTreeScheme::SetLabelVisibility(), CPhyloTreeWidget::SetRotateLabels(), CPhyloTreeWidget::SetScheme(), CPhyloTreeScheme::SetTooltipFormat(), CPhyloTreeWidget::SetUseDistances(), CPhyloTreeDataSource::Sort(), CStopWatch::Start(), and CProjectViewBase::x_GetScope().

Referenced by CPhyTreeView::OnProjectChanged(), and CChangePhyloTreeCommand::Unexecute().

◆ OnBrowseDatabases() void CBLASTSearchOptionsPanel::OnBrowseDatabases ( wxCommandEvent &  event )

Definition at line 761 of file blast_search_options_panel.cpp.

References _ASSERT, CMRUList< T >::AddItem(), database, CBLASTParams::GetCurrDatabase(), CBLASTParams::GetCurrMRUDatabases(), CBLASTDatabases::GetDbMap(), CBLASTDatabases::GetInstance(), CBLAST_DB_Dialog::GetSelectedDatabases(), CBLASTParams::IsSubjNucInput(), kDBBrowserSection, CBLASTDatabases::Loaded(), CBLASTSearchOptionsPanel::m_DatabaseCombo, CBLASTSearchOptionsPanel::m_Params, CAlgoToolManagerParamsPanel::m_RegPath, CBLASTSearchOptionsPanel::m_ToolName, CBLAST_DB_Dialog::SelectDatabases(), CBLAST_DB_Dialog::SetDBMap(), CDialog::SetRegistryPath(), CBLAST_DB_Dialog::SetToolName(), ToStdString(), and CBLASTSearchOptionsPanel::x_UpdateDBCombo().

◆ OnComboboxSelected() void CCleanupAlignmentsParamsPanel::OnComboboxSelected ( wxCommandEvent &  event ) ◆ OnCreateSelectedSubtree() void CPhyTreeView::OnCreateSelectedSubtree ( CEvent *  evt )

Definition at line 1505 of file phy_tree_view.cpp.

References CAppTaskService::AddTask(), IWorkbench::GetAppTaskService(), CPhyloTree::GetCurrentNodeIdx(), CPhyloTree::GetNumSelected(), CRef< C, Locker >::GetPointer(), CTreeModel< TNode >::GetRootIdx(), CPhyloTreeSelectionRoot::GetSelectionRootIdx(), IServiceLocator::GetServiceByType(), CPhyloTreeDataSource::GetTree(), CPhyTreeView::GetWidget(), CPhyTreeView::m_BioTreeContainer, CPhyTreeView::m_DataSource, CPhyTreeView::m_EditUpdate, CProjectViewBase::m_ProjectId, CProjectViewBase::m_Workbench, CTreeModel< CPhyloTreeNode >::Null(), CSelectProjectOptions::Set_AddToExistingProject(), TreeConvert2Container(), TreeConvertSelected2Container(), and TreeDepthFirst().

◆ OnDatabaseComboSelected() void CBLASTSearchOptionsPanel::OnDatabaseComboSelected ( wxCommandEvent &  event ) ◆ OnDSChanged() ◆ OnExplore() void CNetBLASTUIDataSource::OnExplore ( ) ◆ OnExportTree() void CPhyTreeView::OnExportTree ( CEvent *  evt )

Definition at line 1566 of file phy_tree_view.cpp.

References _ASSERT, CAppTaskService::AddTask(), IWorkbench::GetAppTaskService(), CExportTreeDlg::GetData(), CPhyloTreeWidget::GetScheme(), CPhyloTreeDataSource::GetTree(), CPhyTreeView::GetWidget(), CPhyloTreeWidget::HasScheme(), CPhyTreeView::m_DataSource, CProjectViewBase::m_Workbench, CPhyExportParams::SetBioTree(), CPhyExportParams::SetLabelFormat(), CPhyloTreeScheme::SetLabelFormat(), and TreeConvert2Container().

◆ OnFilterInputTextUpdated() void CNetBlastDMSearchFormPanel::OnFilterInputTextUpdated ( wxCommandEvent &  event ) ◆ OnInitDialog() void CBLAST_DB_Dialog::OnInitDialog ( wxInitDialogEvent &  event )

Definition at line 315 of file blast_db_dialog.cpp.

References CBLAST_Dlg_Item::GetId(), CBLAST_Dlg_Item::GetPath(), GUI_AsyncExec(), kEmptyStr, CBLAST_DB_Dialog::m_DbItems, CBLAST_DB_Dialog::m_SelDatabase, CBLAST_DB_Dialog::m_TreeCtrl, NON_CONST_ITERATE, wxT, CBLAST_DB_Dialog::x_CreateItems(), and CBLAST_DB_Dialog::x_FilterItems().

◆ OnLoadRIDs() void CNetBLASTUIDataSource::OnLoadRIDs ( ) ◆ OnLocalDBLoaderClick() void CBLASTSearchOptionsPanel::OnLocalDBLoaderClick ( wxCommandEvent &  event ) ◆ OnMusclePathClick() void CMuscleToolPanel::OnMusclePathClick ( wxCommandEvent &  event ) ◆ OnNucRadioSelected() void CBLASTSearchOptionsPanel::OnNucRadioSelected ( wxCommandEvent &  event ) ◆ OnOkClick() void CBLAST_DB_Dialog::OnOkClick ( wxCommandEvent &  event ) ◆ OnOpenGraphicalView() void CMultiAlignView::OnOpenGraphicalView ( CEvent *  evt ) ◆ OnProgramComboSelected() void CBLASTSearchOptionsPanel::OnProgramComboSelected ( wxCommandEvent &  event ) ◆ OnProjectChanged() [1/8] void CMPCrossAlignView::OnProjectChanged ( ) virtual ◆ OnProjectChanged() [2/8] void CMultiAlignView::OnProjectChanged ( ) virtual

Reimplemented from CProjectViewBase.

Definition at line 245 of file multi_align_view.cpp.

References _ASSERT, CObjectIndex::Clear(), CAlnMultiDSBuilder::CreateDataSource(), CAlnUserOptions::fAllowTranslocation, CAlnUserOptions::fSkipSortByScore, CAlnMultiDSBuilder::Init(), CMultiAlignView::m_AlnWidget, CMultiAlignView::m_Builder, CMultiAlignView::m_DataSource, CMultiAlignView::m_ObjIndex, CMultiAlignView::m_OrigAlign, CMultiAlignView::m_OrigAnnot, CMultiAlignView::m_Sparse, NULL, CAlnMultiDSBuilder::PreCreateDataSource(), CAlnMultiWidget::SetDataSource(), CAlnMultiDSBuilder::SetListener(), CAlnUserOptions::SetMergeFlags(), CAlnMultiDSBuilder::SetOptions(), CProjectViewBase::x_GetScope(), CProjectViewBase::x_HasProject(), and CProjectViewBase::x_UpdateContentLabel().

Referenced by CMultiAlignView::InitView().

◆ OnProjectChanged() [3/8] ◆ OnProjectChanged() [4/8] ◆ OnProjectChanged() [5/8] ◆ OnProjectChanged() [6/8] ◆ OnProjectChanged() [7/8] ◆ OnProjectChanged() [8/8]

Reimplemented from CProjectViewBase.

Definition at line 933 of file phy_tree_view.cpp.

References _ASSERT, CObjectIndex::Clear(), CProjectViewEvent::eDataChanging, CConstRef< C, Locker >::Empty(), CPhyloTreeDataSource::GenerateTooltipFormat(), CProjectViewEvent::GetSubtype(), CPhyTreeView::GetWidget(), CPhyTreeView::m_BioTreeContainer, CPhyTreeView::m_DataSource, CPhyTreeView::m_EditUpdate, CPhyTreeView::m_ObjectIndex, CPhyTreeView::m_Scheme, NULL, CPhyTreeView::OnBioTreeChanged(), CPhyloTreeWidget::RedrawDataSource(), CPhyloTreeScheme::SetTooltipFormat(), CProjectViewBase::x_HasProject(), and CProjectViewBase::x_UpdateContentLabel().

◆ OnProtRadioSelected() void CBLASTSearchOptionsPanel::OnProtRadioSelected ( wxCommandEvent &  event ) ◆ OnQuerySequenceSetSelected() void CBLASTSearchOptionsPanel::OnQuerySequenceSetSelected ( wxCommandEvent &  event ) ◆ OnRepeatTypeSelected() void CBLASTSearchParamsPanel::OnRepeatTypeSelected ( wxCommandEvent &  event ) ◆ OnResetBtnClick() void CBLAST_DB_Dialog::OnResetBtnClick ( wxCommandEvent &  event ) ◆ OnResetClick() void CNetBlastDMSearchFormPanel::OnResetClick ( wxCommandEvent &  event ) ◆ OnSearchTextUpdated() void CBLAST_DB_Dialog::OnSearchTextUpdated ( wxCommandEvent &  event ) ◆ OnSelectLocalDB() void CBLASTSearchOptionsPanel::OnSelectLocalDB ( wxCommandEvent &  event ) ◆ OnSomethingEdited() void CPhyTreeView::OnSomethingEdited ( CEvent *  evt )

Definition at line 1592 of file phy_tree_view.cpp.

References CUser_object::AddField(), CUser_object_Base::CanGetType(), command, CObject_id_Base::e_not_set, eCmdFeaturesEdited, eCmdGrpExpandCollapse, eCmdLabelFormatChanged, eCmdNodeExpandCollapse, eCmdRenderingOptionsChanged, eCmdTreeLabelSet, CStopWatch::Elapsed(), ICommandProccessor::Execute(), CEvent::GetAttachment(), CPhyloTreeWidget::GetCurrRenderer(), CUser_field_Base::GetData(), CPhyloTreeWidget::GetDS(), CUser_object::GetField(), CEvent::GetID(), CConstRef< C, Locker >::GetPointer(), CPhyloTreeWidget::GetRotateLabels(), CPhyloTreeWidget::GetScheme(), CPhyloTreeDataSource::GetTree(), CPhyloTreeDataSource::GetTreeLabel(), CUser_object_Base::GetType(), CPhyloTreeWidget::GetUseDistances(), CPhyTreeView::GetWidget(), CUser_object::HasField(), CPhyloTreeWidget::HasScheme(), CUser_field_Base::C_Data::IsBool(), CUser_field_Base::C_Data::IsInt(), CUser_object_Base::IsSetType(), CUser_field_Base::C_Data::IsStr(), CPhyTreeView::m_BioTreeContainer, m_CreateProperyUndoCommand, m_CreateUndoCommand, CPhyTreeView::m_DataSource, CPhyTreeView::m_EditUpdate, m_ExecutePropertyCommand, m_ExecuteUndoCommand, CPhyTreeView::m_Scheme, NULL, CRef< C, Locker >::Reset(), CStopWatch::Restart(), CTreeLabel::SaveToUserObject(), CUser_field_Base::SetData(), CUser_object::SetField(), CPhyloTreeScheme::SetLabelFormat(), CObject_id_Base::SetStr(), CUser_object_Base::SetType(), CBioTreeContainer_Base::SetUser(), CStopWatch::Start(), TreeConvert2Container(), CObject_id_Base::Which(), and CProjectView::x_GetUndoManager().

◆ OnStandaloneClick() void CBLASTSearchParamsPanel::OnStandaloneClick ( wxCommandEvent &  event ) ◆ OnSubjectLocalDBSelected() void CBLASTSearchOptionsPanel::OnSubjectLocalDBSelected ( wxCommandEvent &  event ) ◆ OnSubjectNCBIDBSelected() void CBLASTSearchOptionsPanel::OnSubjectNCBIDBSelected ( wxCommandEvent &  event ) ◆ OnSubjectSequenceSetSelected() void CBLASTSearchOptionsPanel::OnSubjectSequenceSetSelected ( wxCommandEvent &  event ) ◆ OnSubjectSequencesSelected() void CBLASTSearchOptionsPanel::OnSubjectSequencesSelected ( wxCommandEvent &  event ) ◆ OnSubmittedCheckClick() void CNetBlastDMSearchFormPanel::OnSubmittedCheckClick ( wxCommandEvent &  event ) ◆ OnTimer() void CBLASTSearchOptionsPanel::OnTimer ( wxTimerEvent &  event ) protected ◆ OnTreectrlItemActivated() void CBLAST_DB_Dialog::OnTreectrlItemActivated ( wxTreeEvent &  event ) ◆ OnTreectrlItemCollapsed() void CBLAST_DB_Dialog::OnTreectrlItemCollapsed ( wxTreeEvent &  event ) ◆ OnTreectrlItemExpanded() void CBLAST_DB_Dialog::OnTreectrlItemExpanded ( wxTreeEvent &  event ) ◆ OnTreectrlSelChanged() void CBLAST_DB_Dialog::OnTreectrlSelChanged ( wxTreeEvent &  event ) ◆ OnTryAgain() void CBLASTSearchOptionsPanel::OnTryAgain ( wxCommandEvent &  event ) protected ◆ OnVisibleRangeChanged() [1/3]

Reimplemented from CProjectView.

Definition at line 330 of file cross_align_view.cpp.

References CGlRect< T >::Bottom(), CVisibleRange::Clamp(), CCrossAlnWidget::GetPort(), CGlPane::GetVisibleRect(), CGlRect< T >::Left(), CCrossAlignView::m_AlnWidget, CCrossAlignView::m_DataSource, CVisibleRange::Match(), CGlRect< T >::Right(), CRange_Base::SetFrom(), CCrossAlnWidget::SetQueryVisibleRange(), CCrossAlnWidget::SetSubjectVisibleRange(), CRange_Base::SetTo(), and CGlRect< T >::Top().

◆ OnVisibleRangeChanged() [2/3]

Reimplemented from CProjectView.

Definition at line 336 of file dot_matrix_view.cpp.

References CGlRect< T >::Bottom(), CVisibleRange::Clamp(), CHitMatrixWidget::GetPort(), CGlPane::GetVisibleRect(), CGlRect< T >::Left(), CDotMatrixView::m_AlnWidget, CDotMatrixView::m_DataSource, CVisibleRange::Match(), CGlRect< T >::Right(), CRange_Base::SetFrom(), CHitMatrixWidget::SetQueryVisibleRange(), CHitMatrixWidget::SetSubjectVisibleRange(), CRange_Base::SetTo(), and CGlRect< T >::Top().

◆ OnVisibleRangeChanged() [3/3] ◆ OnWidgetRangeChanged() void CAlignSpanView::OnWidgetRangeChanged ( ) virtual ◆ OnWidgetSelChanged() void CAlignSpanView::OnWidgetSelChanged ( ) virtual ◆ OnWindowmaskerTaxIdSelected() void CBLASTSearchParamsPanel::OnWindowmaskerTaxIdSelected ( wxCommandEvent &  event ) ◆ OnWMDownload() void CBLASTSearchParamsPanel::OnWMDownload ( wxCommandEvent &  event ) ◆ Open() bool CNetBLASTUIDataSource::Open ( ) virtual

Prepares Data Source for use, any initialization that can be potentially time-consuming or may require error handling shall be done in this function, not in a constructor.

Is initialization takes more than 1-2 sec it shall be done on a background thread (see App Job Dispatcher).

Implements IUIDataSource.

Definition at line 224 of file net_blast_ui_data_source.cpp.

References NStr::DoubleToString(), CStopWatch::Elapsed(), ERR_POST, CBLASTDatabases::GetInstance(), CExtensionRegistry::GetInstance(), Info(), kAppExpCmdExtPoint, kCmdExtPoint, CBLASTDatabases::Load(), CNetBLASTUIDataSource::m_Open, CSysPath::ResolvePath(), CStopWatch::Start(), sw, t, wxT, CNetBLASTUIDataSource::x_AutoStartMonitoring(), and CNetBLASTUIDataSource::x_LoadJobDescriptors().

◆ operator=() [1/12] ◆ operator=() [2/12] ◆ operator=() [3/12] ◆ operator=() [4/12] ◆ operator=() [5/12] ◆ operator=() [6/12] ◆ operator=() [7/12] ◆ operator=() [8/12] ◆ operator=() [9/12] ◆ operator=() [10/12] ◆ operator=() [11/12] ◆ operator=() [12/12] ◆ operator==() [1/11] ◆ operator==() [2/11] ◆ operator==() [3/11] ◆ operator==() [4/11] ◆ operator==() [5/11] ◆ operator==() [6/11] ◆ operator==() [7/11] ◆ operator==() [8/11] ◆ operator==() [9/11] ◆ operator==() [10/11] ◆ operator==() [11/11] ◆ PostExecute() bool CTextAlignObjectLoader::PostExecute ( ) virtual ◆ PreExecute() bool CTextAlignObjectLoader::PreExecute ( ) virtual ◆ PrintParams() void CBLASTParams::PrintParams ( const string &  log_title ) const

LOG_POST params for forensic purposes.

Definition at line 1188 of file blast_search_params.cpp.

References CBLASTParams::GetAdvancedParams(), CBLASTParams::GetCurrDatabase(), CBLASTParams::GetCurrParams(), CBLASTParams::GetCurrProgram(), CBLASTParams::GetEntrezQuery(), CBLASTParams::GetProgramLabel(), Info(), LOG_POST, CBLASTParams::SProgParams::m_DbGeneticCode, CBLASTParams::SProgParams::m_eValue, CBLASTParams::SProgParams::m_FilterLowComplex, CBLASTParams::SProgParams::m_MaskLowercase, CBLASTParams::SProgParams::m_MaskRepeats, CBLASTParams::SProgParams::m_QueryGeneticCode, CBLASTParams::SProgParams::m_RepeatLib, CBLASTParams::SProgParams::m_Threshold, and CBLASTParams::SProgParams::m_WordSize.

Referenced by CBLASTToolManager::GetTask().

◆ ProgressCallback() bool CCreateNeedlemanWunschJob::ProgressCallback ( const string &  status, float  done  ) ◆ QuickLaunch() [1/5] IAppTask * CBLASTToolManager::QuickLaunch ( ) virtual

Implements IUIAlgoToolManager.

Definition at line 361 of file blast_tool_manager.cpp.

References map_checker< Container >::begin(), copy(), SProjectSelectorParams::eAddToExistingProject, SProjectSelectorParams::eCreateOneProject, CBLASTParams::eNCBIDB, map_checker< Container >::end(), map_checker< Container >::find(), CBLASTToolManager::GetBLASTDataSource(), CProjectService::GetObjProjects(), CBLASTParams::GetSeqLocs(), IServiceLocator::GetServiceByType(), CBLASTParams::GetSubjectType(), CBLASTToolManager::GetTask(), i, CBLASTParams::IsNucInput(), kSelectedSequences, SProjectSelectorParams::m_CreateFolder, SProjectSelectorParams::m_FolderName, CBLASTToolManager::m_NucObjects, CBLASTToolManager::m_Params, SProjectSelectorParams::m_ProjectMode, CBLASTToolManager::m_ProtObjects, SProjectSelectorParams::m_SelectedProjectId, CBLASTToolManager::m_SrvLocator, CBLASTToolManager::m_UseNucForMixInput, CBLASTToolManager::x_IsNucInput(), and CBLASTToolManager::x_SelectCompatibleInputObjects().

◆ QuickLaunch() [2/5]

Reimplemented from CAlgoToolManagerBase.

Definition at line 131 of file kalign_tool.cpp.

References map_checker< Container >::empty(), CProjectService::GetObjProjects(), IServiceLocator::GetServiceByType(), CKalignTool::m_Objects, CKalignTool::m_Params, CAlgoToolManagerBase::m_SrvLocator, NON_CONST_ITERATE, NULL, CRef< C, Locker >::Release(), CSelectProjectOptions::Set_AddToExistingProject(), CSelectProjectOptions::Set_CreateNewProject(), CKalignToolParams::SetObjects(), wxT, CKalignTool::x_CreateLoadingJob(), and CKalignTool::x_SelectCompatibleInputObjects().

◆ QuickLaunch() [3/5]

Reimplemented from CAlgoToolManagerBase.

Definition at line 131 of file mafft_tool.cpp.

References map_checker< Container >::empty(), CProjectService::GetObjProjects(), IServiceLocator::GetServiceByType(), CMafftTool::m_Objects, CMafftTool::m_Params, CAlgoToolManagerBase::m_SrvLocator, NON_CONST_ITERATE, NULL, CRef< C, Locker >::Release(), CSelectProjectOptions::Set_AddToExistingProject(), CSelectProjectOptions::Set_CreateNewProject(), CMafftToolParams::SetObjects(), wxT, CMafftTool::x_CreateLoadingJob(), and CMafftTool::x_SelectCompatibleInputObjects().

◆ QuickLaunch() [4/5]

Reimplemented from CAlgoToolManagerBase.

Definition at line 131 of file muscle_tool.cpp.

References map_checker< Container >::empty(), CProjectService::GetObjProjects(), IServiceLocator::GetServiceByType(), CMuscleTool::m_Objects, CMuscleTool::m_Params, CAlgoToolManagerBase::m_SrvLocator, NON_CONST_ITERATE, NULL, CRef< C, Locker >::Release(), CSelectProjectOptions::Set_AddToExistingProject(), CSelectProjectOptions::Set_CreateNewProject(), CMuscleToolParams::SetObjects(), wxT, CMuscleTool::x_CreateLoadingJob(), and CMuscleTool::x_SelectCompatibleInputObjects().

◆ QuickLaunch() [5/5]

Reimplemented from CAlgoToolManagerBase.

Definition at line 270 of file splign_tool.cpp.

References copy(), map_checker< Container >::empty(), CProjectService::GetObjProjects(), IServiceLocator::GetServiceByType(), CSplignTool::m_GenomicObjects, CSplignTool::m_NAObjects, CAlgoToolManagerBase::m_SrvLocator, NON_CONST_ITERATE, CRef< C, Locker >::Release(), CSelectProjectOptions::Set_AddToExistingProject(), CSelectProjectOptions::Set_CreateNewProject(), wxT, CSplignTool::x_CreateLoadingJob(), and CSplignTool::x_SelectCompatibleInputObjects().

◆ RebuildObjectIndex() void CPhyTreeView::RebuildObjectIndex ( ) ◆ RecognizeFormat() [1/4] ◆ RecognizeFormat() [2/4] ◆ RecognizeFormat() [3/4] bool CPslLoadManager::RecognizeFormat ( const wxString &  filename ) virtual ◆ RecognizeFormat() [4/4] bool CTextAlignLoaderManager::RecognizeFormat ( const wxString &  filename ) virtual ◆ RegisterCommands() [1/5] ◆ RegisterCommands() [2/5] ◆ RegisterCommands() [3/5] ◆ RegisterCommands() [4/5] ◆ RegisterCommands() [5/5] ◆ RegisterIconAliases() [1/7] ◆ RegisterIconAliases() [2/7] ◆ RegisterIconAliases() [3/7] ◆ RegisterIconAliases() [4/7] ◆ RegisterIconAliases() [5/7] ◆ RegisterIconAliases() [6/7] ◆ RegisterIconAliases() [7/7] ◆ Release() void CNetBlastJobDescriptor::Release ( void  ) ◆ RequestCancel() void CBLASTSeqToolJob::RequestCancel ( ) virtual ◆ ResetCurrParams() void CBLASTParams::ResetCurrParams ( ) ◆ RestartSearch() void CNetBlastDMSearchFormPanel::RestartSearch ( ) ◆ RestoreDefaults() [1/12] void CBLASTSearchOptionsPanel::RestoreDefaults ( ) virtual ◆ RestoreDefaults() [2/12] void CBLASTSearchParamsPanel::RestoreDefaults ( ) virtual ◆ RestoreDefaults() [3/12] void CBLASTToolManager::RestoreDefaults ( ) virtual ◆ RestoreDefaults() [4/12] void CCleanupAlignmentsParamsPanel::RestoreDefaults ( ) virtual ◆ RestoreDefaults() [5/12] void CFindOverlapPanel::RestoreDefaults ( ) virtual ◆ RestoreDefaults() [6/12] void CGroupAlignmentsParamsPanel::RestoreDefaults ( ) virtual ◆ RestoreDefaults() [7/12] void CMergeAlignmentsParamsPanel::RestoreDefaults ( ) virtual ◆ RestoreDefaults() [8/12] void CSplignPanel::RestoreDefaults ( ) virtual ◆ RestoreDefaults() [9/12] void CTreeBuilderPanel::RestoreDefaults ( ) virtual ◆ RestoreDefaults() [10/12] void CMuscleToolPanel::RestoreDefaults ( ) virtual ◆ RestoreDefaults() [11/12] void CNGAlignPanel::RestoreDefaults ( ) virtual ◆ RestoreDefaults() [12/12] void CTaxTreeToolPanel::RestoreDefaults ( ) virtual ◆ Retrieve() ◆ Run() [1/2]

Function that does all the useful work, called by the Engine.

Run() shall be implemented so that it will allow for exiting once RequestCancel() is called.

Implements IAppJob.

Definition at line 86 of file blast_jobs.cpp.

References IAppJob::eCompleted, IAppJob::eFailed, Error(), CNetBlastSubmittingJob::GetDescr(), CException::GetMsg(), ITERATE, LOG_POST, CNetBlastSubmittingJob::m_Error, CNetBlastSubmittingJob::m_Errors, CNetBlastSubmittingJob::m_Mutex, CException::ReportAll(), CRef< C, Locker >::Reset(), CNetBlastSubmittingJob::x_ResetState(), and CNetBlastSubmittingJob::x_Run().

◆ Run() [2/2]

Function that does all the useful work, called by the Engine.

Run() shall be implemented so that it will allow for exiting once RequestCancel() is called.

Implements IAppJob.

Definition at line 285 of file blast_jobs.cpp.

References IAppJob::eFailed, Error(), CNetBlastMonitoringJob::GetDescr(), CException::GetMsg(), ITERATE, LOG_POST, CNetBlastMonitoringJob::m_Error, CNetBlastMonitoringJob::m_Errors, CNetBlastMonitoringJob::m_Mutex, CException::ReportAll(), CRef< C, Locker >::Reset(), CNetBlastMonitoringJob::x_ResetState(), and CNetBlastMonitoringJob::x_Run().

◆ s_AssignFeatureIds() void CCreateGeneModelTask::s_AssignFeatureIds ( objects::CSeq_annot &  annot, objects::CObject_id::TId &  max_id  ) static ◆ s_BlastInterrupt() ◆ s_CreateDBXref() void SGeneCdsmRnaFeats::s_CreateDBXref ( const objects::CSeq_feat &  from_feat, objects::CSeq_feat &  to_feat, const string &  dbname  ) static ◆ s_CreateXRefLink() void SGeneCdsmRnaFeats::s_CreateXRefLink ( objects::CSeq_feat &  from_feat, objects::CSeq_feat &  to_feat  ) static ◆ s_FeaturesHaveIDs() bool CCreateGeneModelTask::s_FeaturesHaveIDs ( const objects::CSeq_annot &  annot ) static ◆ s_FeaturesHaveXrefs() bool CCreateGeneModelTask::s_FeaturesHaveXrefs ( const objects::CSeq_annot &  annot ) static ◆ s_FindHighestFeatId() ◆ s_GetGeneID() ◆ SaveSettings() [1/33] void CAlignSpanView::SaveSettings ( ) const virtual ◆ SaveSettings() [2/33] void CBLASTSearchOptionsPanel::SaveSettings ( ) const virtual ◆ SaveSettings() [3/33] virtual void CBLASTSearchParamsPanel::SaveSettings ( ) const inlinevirtual ◆ SaveSettings() [4/33] void CBLASTToolManager::SaveSettings ( ) const virtual

Implements IRegSettings.

Definition at line 544 of file blast_tool_manager.cpp.

References map_checker< Container >::empty(), CGuiRegistry::GetInstance(), CGuiRegistry::GetWriteView(), CBLASTParams::IsNucInput(), kParamsTag, kUseNucForMixInput, CBLASTToolManager::m_NucObjects, CBLASTToolManager::m_OptionsPanel, CBLASTToolManager::m_Params, CBLASTToolManager::m_ProtObjects, CBLASTToolManager::m_RegPath, CBLASTToolManager::m_UseNucForMixInput, CGuiRegistryUtil::MakeKey(), CBLASTSearchOptionsPanel::SaveSettings(), CRegistryWriteView::Set(), CUser_field_Base::SetData(), CRegistryWriteView::SetField(), and CBLASTParams::ToUserObject().

◆ SaveSettings() [5/33] void SCleanupAlignmentsParams::SaveSettings ( ) const virtual ◆ SaveSettings() [6/33] void CCleanupAlignmentsParamsPanel::SaveSettings ( ) const virtual ◆ SaveSettings() [7/33] void CClustalOmegaToolParams::SaveSettings ( ) const virtual

Implements IRegSettings.

Definition at line 102 of file clustal_omega_tool_params.cpp.

References FnToStdString(), CGuiRegistry::GetInstance(), CGuiRegistry::GetWriteView(), kClustalwPath, kCommandLine, kGenerateTree, CClustalOmegaToolParams::m_ClustalOmegaPath, CClustalOmegaToolParams::m_CommandLine, CClustalOmegaToolParams::m_GenerateTree, CClustalOmegaToolParams::m_RegPath, CRegistryWriteView::Set(), CGuiRegistry::Set(), and ToStdString().

◆ SaveSettings() [8/33] void CClustalwToolParams::SaveSettings ( ) const virtual

Implements IRegSettings.

Definition at line 92 of file clustalw_tool_params.cpp.

References FnToStdString(), CGuiRegistry::GetInstance(), CGuiRegistry::GetWriteView(), kClustalwPath, kCommandLine, kGenerateTree, CClustalwToolParams::m_ClustalWPath, CClustalwToolParams::m_CommandLine, CClustalwToolParams::m_GenerateTree, CClustalwToolParams::m_RegPath, CRegistryWriteView::Set(), CGuiRegistry::Set(), and ToStdString().

◆ SaveSettings() [9/33] void CFindOverlapPanel::SaveSettings ( ) const virtual ◆ SaveSettings() [10/33] void CFindOverlapParams::SaveSettings ( ) const virtual

IRegSettings.

Implements IRegSettings.

Definition at line 89 of file find_overlap_params.cpp.

References CGuiRegistry::GetInstance(), CGuiRegistry::GetWriteView(), kBlastParamsTag, kFilterTag, kMaxSlopTag, CFindOverlapParams::m_BlastParams, CFindOverlapParams::m_FilterQty, CFindOverlapParams::m_MaxSlop, CFindOverlapParams::m_RegPath, CRegistryWriteView::Set(), and ToStdString().

◆ SaveSettings() [11/33] void SGroupAlignmentsParams::SaveSettings ( ) const virtual

Implements IRegSettings.

Definition at line 98 of file group_alignments_params_panel.cpp.

References CGuiRegistry::GetInstance(), CGuiRegistry::GetWriteView(), kGroupByEST, kGroupByHTGS, kGroupByLikeTaxId, kGroupByPatent, kGroupByPredictedRefSeq, kGroupByRefSeq, kGroupBySeqId, kGroupByStrand, kGroupByTaxId, kGroupByWGS, SGroupAlignmentsParams::m_GroupByEST, SGroupAlignmentsParams::m_GroupByHTGS, SGroupAlignmentsParams::m_GroupByLikeTaxId, SGroupAlignmentsParams::m_GroupByPatent, SGroupAlignmentsParams::m_GroupByPredictedRefSeq, SGroupAlignmentsParams::m_GroupByRefSeq, SGroupAlignmentsParams::m_GroupBySeqId, SGroupAlignmentsParams::m_GroupByStrand, SGroupAlignmentsParams::m_GroupByTaxId, SGroupAlignmentsParams::m_GroupByWGS, SGroupAlignmentsParams::m_RegPath, and CRegistryWriteView::Set().

◆ SaveSettings() [12/33] void CGroupAlignmentsParamsPanel::SaveSettings ( ) const virtual ◆ SaveSettings() [13/33] void CKalignToolParams::SaveSettings ( ) const virtual

Implements IRegSettings.

Definition at line 98 of file kalign_tool_params.cpp.

References CGuiRegistry::GetInstance(), CGuiRegistry::GetWriteView(), kAlignPath, kCommandLine, kQuietMode, CKalignToolParams::m_CommandLine, CKalignToolParams::m_KalignPath, CKalignToolParams::m_QuietFlag, CKalignToolParams::m_RegPath, CRegistryWriteView::Set(), CGuiRegistry::Set(), and ToStdString().

◆ SaveSettings() [14/33] void CMafftToolParams::SaveSettings ( ) const virtual

Implements IRegSettings.

Definition at line 102 of file mafft_tool_params.cpp.

References CGuiRegistry::GetInstance(), CGuiRegistry::GetWriteView(), kAutoFlag, kCommandLine, kMafftPath, kQuietMode, CMafftToolParams::m_AutoFlag, CMafftToolParams::m_CommandLine, CMafftToolParams::m_MafftPath, CMafftToolParams::m_QuietFlag, CMafftToolParams::m_RegPath, CRegistryWriteView::Set(), CGuiRegistry::Set(), and ToStdString().

◆ SaveSettings() [15/33] void SMergeAlignmentsParams::SaveSettings ( ) const virtual

Implements IRegSettings.

Definition at line 79 of file merge_alignments_params_panel.cpp.

References CGuiRegistry::GetInstance(), CGuiRegistry::GetWriteView(), kDirectionTag, kFillUnalignedTag, kMergeAlgoTag, kMergeFlagsTag, SMergeAlignmentsParams::m_Direction, SMergeAlignmentsParams::m_FillUnaligned, SMergeAlignmentsParams::m_MergeAlgo, SMergeAlignmentsParams::m_MergeFlags, SMergeAlignmentsParams::m_RegPath, and CRegistryWriteView::Set().

◆ SaveSettings() [16/33] void CMergeAlignmentsParamsPanel::SaveSettings ( ) const virtual ◆ SaveSettings() [17/33] void CMultiAlignView::SaveSettings ( ) const virtual ◆ SaveSettings() [18/33] void CMuscleToolParams::SaveSettings ( ) const virtual

Implements IRegSettings.

Definition at line 102 of file muscle_tool_params.cpp.

References CGuiRegistry::GetInstance(), CGuiRegistry::GetWriteView(), kCommandLine, kGenerateTree, kMusclePath, kScoringMethod, CMuscleToolParams::m_CommandLine, CMuscleToolParams::m_GenerateTree, CMuscleToolParams::m_MusclePath, CMuscleToolParams::m_RegPath, CMuscleToolParams::m_ScoringMethod, CRegistryWriteView::Set(), CGuiRegistry::Set(), and ToStdString().

◆ SaveSettings() [19/33] void CNeedlemanWunschToolParams::SaveSettings ( ) const virtual

Implements IRegSettings.

Definition at line 104 of file needlemanwunsch_tool_params.cpp.

References CGuiRegistry::GetInstance(), CGuiRegistry::GetWriteView(), kBandSize, kFirstSeqFreeEnds, kGapExtendCost, kGapOpenCost, kMatchCost, kMismatchCost, kSecondSeqFreeEnds, CNeedlemanWunschToolParams::m_BandSize, CNeedlemanWunschToolParams::m_FirstSeqFreeEnds, CNeedlemanWunschToolParams::m_GapExtendCost, CNeedlemanWunschToolParams::m_GapOpenCost, CNeedlemanWunschToolParams::m_MatchCost, CNeedlemanWunschToolParams::m_MismatchCost, CNeedlemanWunschToolParams::m_RegPath, CNeedlemanWunschToolParams::m_SecondSeqFreeEnds, and CRegistryWriteView::Set().

◆ SaveSettings() [20/33] void CNetBLASTUIDataSource::SaveSettings ( ) const virtual ◆ SaveSettings() [21/33] void CNetBLASTUILoadManager::SaveSettings ( ) const virtual

Implements IRegSettings.

Definition at line 220 of file net_blast_ui_load_manager.cpp.

References CNetBLASTLoadOptionPanel::GetInput(), CGuiRegistry::GetInstance(), CGuiRegistry::GetWriteView(), kProjectParamsTag, kRIDsInputTag, CNetBLASTUILoadManager::m_OptionPanel, CNetBLASTUILoadManager::m_ProjectParams, CNetBLASTUILoadManager::m_RegPath, CNetBLASTUILoadManager::m_SavedInput, SProjectSelectorParams::SaveSettings(), and CRegistryWriteView::Set().

◆ SaveSettings() [22/33] void CNGAlignParams::SaveSettings ( ) const virtual

Implements IRegSettings.

Definition at line 115 of file ngalign_params.cpp.

References CGuiRegistry::GetInstance(), CGuiRegistry::GetWriteView(), kAdvParams, kBestHit, keValue, kFilterMode, kJobTitle, kWM_TaxId, kWordSize, CNGAlignParams::m_AdvParams, CNGAlignParams::m_BestHit, CNGAlignParams::m_eValue, CNGAlignParams::m_FilterMode, CNGAlignParams::m_JobTitle, CNGAlignParams::m_RegPath, CNGAlignParams::m_WM_TaxId, CNGAlignParams::m_WordSize, CRegistryWriteView::Set(), and ToStdString().

◆ SaveSettings() [23/33] void CPhyTreeView::SaveSettings ( ) const virtual ◆ SaveSettings() [24/33] void CSplignPanel::SaveSettings ( ) const virtual ◆ SaveSettings() [25/33] void CSplignParams::SaveSettings ( ) const virtual

Implements IRegSettings.

Definition at line 112 of file splign_params.cpp.

References CGuiRegistry::GetInstance(), CGuiRegistry::GetWriteView(), kcDNA_strandTag, kCompPenaltyTag, kDiscType, kEndGapDetectTag, kMaxGenomicExtentTag, kMaxIntron, kMinCompIdentityTag, kMinExonIdentityTag, kPolyADetectTag, CSplignParams::m_cDNA_strand, CSplignParams::m_CompPenalty, CSplignParams::m_DiscType, CSplignParams::m_EndGapDetect, CSplignParams::m_MaxGenomicExtent, CSplignParams::m_MaxIntron, CSplignParams::m_MinCompIdentity, CSplignParams::m_MinExonIdentity, CSplignParams::m_PolyADetect, CSplignParams::m_RegPath, and CRegistryWriteView::Set().

◆ SaveSettings() [26/33] void CTaxTreeToolParams::SaveSettings ( ) const virtual ◆ SaveSettings() [27/33] void CTreeBuilderPanel::SaveSettings ( ) const virtual ◆ SaveSettings() [28/33] void CTreeBuilderParams::SaveSettings ( ) const virtual

IRegSettings.

Implements IRegSettings.

Definition at line 86 of file tree_builder_params.cpp.

References CGuiRegistry::GetInstance(), CGuiRegistry::GetWriteView(), kConsTag, kDistTag, kLeafTag, CTreeBuilderParams::m_ConstructMethod, CTreeBuilderParams::m_DistanceMethod, CTreeBuilderParams::m_LeafLabels, CTreeBuilderParams::m_RegPath, CRegistryWriteView::Set(), and ToStdString().

◆ SaveSettings() [29/33] void CMuscleToolPanel::SaveSettings ( ) const virtual ◆ SaveSettings() [30/33] void CNGAlignPanel::SaveSettings ( ) const virtual ◆ SaveSettings() [31/33] void CPslLoadManager::SaveSettings ( ) const virtual ◆ SaveSettings() [32/33] void CTaxTreeToolPanel::SaveSettings ( ) const virtual ◆ SaveSettings() [33/33] void CTextAlignLoaderManager::SaveSettings ( ) const virtual ◆ SCleanupAlignmentsParams() SCleanupAlignmentsParams::SCleanupAlignmentsParams ( ) ◆ SelectDatabases() void CBLAST_DB_Dialog::SelectDatabases ( vector< string > &  databases ) ◆ SelectInputType() void CBLASTSearchOptionsPanel::SelectInputType ( ) ◆ SetAdvParams() [1/2] void CBLASTSearchParamsPanel::SetAdvParams ( wxString  value ) inline ◆ SetAdvParams() [2/2] void CNGAlignParams::SetAdvParams ( wxString  value ) inline ◆ SetAutoFlag() void CMafftToolParams::SetAutoFlag ( bool  value ) inline ◆ SetBandSize() void CNeedlemanWunschToolParams::SetBandSize ( int  value ) inline ◆ SetBestHit() void CNGAlignParams::SetBestHit ( bool  value ) inline ◆ SetBlastParams() void CFindOverlapParams::SetBlastParams ( wxString  value ) inline ◆ SetCDNASeqs() ◆ SetCDNAStrand() void CSplignParams::SetCDNAStrand ( int  value ) inline ◆ SetClustalOmegaPath() void CClustalOmegaToolParams::SetClustalOmegaPath ( wxString  value ) inline ◆ SetClustalWPath() void CClustalwToolParams::SetClustalWPath ( wxString  value ) inline ◆ SetCommandLine() [1/5] void CClustalOmegaToolParams::SetCommandLine ( wxString  value ) inline ◆ SetCommandLine() [2/5] void CClustalwToolParams::SetCommandLine ( wxString  value ) inline ◆ SetCommandLine() [3/5] void CKalignToolParams::SetCommandLine ( wxString  value ) inline ◆ SetCommandLine() [4/5] void CMafftToolParams::SetCommandLine ( wxString  value ) inline ◆ SetCommandLine() [5/5] void CMuscleToolParams::SetCommandLine ( wxString  value ) inline ◆ SetCompleted() void CNetBlastDMSearchFormPanel::SetCompleted ( bool  value ) inline ◆ SetCompPenalty() void CSplignParams::SetCompPenalty ( double  value ) inline ◆ SetConstructMethod() void CTreeBuilderParams::SetConstructMethod ( wxString  value ) inline ◆ SetData() [1/5] ◆ SetData() [2/5] ◆ SetData() [3/5] ◆ SetData() [4/5] ◆ SetData() [5/5] ◆ SetDataSource() ◆ SetDbGeneticCode() void CBLASTSearchParamsPanel::SetDbGeneticCode ( wxString  value ) inline ◆ SetDBMap() ◆ SetDiscType() void CSplignParams::SetDiscType ( int  value ) inline ◆ SetDistanceMethod() void CTreeBuilderParams::SetDistanceMethod ( wxString  value ) inline ◆ SetEndGapDetect() void CSplignParams::SetEndGapDetect ( bool  value ) inline ◆ SetEValue() [1/2] void CBLASTSearchParamsPanel::SetEValue ( double  value ) inline ◆ SetEValue() [2/2] void CNGAlignParams::SetEValue ( double  value ) inline ◆ SetExpired() void CNetBlastDMSearchFormPanel::SetExpired ( bool  value ) inline ◆ SetFailed() void CNetBlastDMSearchFormPanel::SetFailed ( bool  value ) inline ◆ SetFilenames() [1/2] void CPslLoadManager::SetFilenames ( const vector< wxString > &  filenames ) virtual ◆ SetFilenames() [2/2] void CTextAlignLoaderManager::SetFilenames ( const vector< wxString > &  filenames ) virtual ◆ SetFilterLowComplex() void CBLASTSearchParamsPanel::SetFilterLowComplex ( bool  value ) inline ◆ SetFilterMode() void CNGAlignParams::SetFilterMode ( int  value ) inline ◆ SetFilterQuality() void CFindOverlapParams::SetFilterQuality ( int  value ) inline ◆ SetFirstSeqFreeEnds() void CNeedlemanWunschToolParams::SetFirstSeqFreeEnds ( int  value ) inline ◆ SetGapExtendCost() void CNeedlemanWunschToolParams::SetGapExtendCost ( int  value ) inline ◆ SetGapOpenCost() void CNeedlemanWunschToolParams::SetGapOpenCost ( int  value ) inline ◆ SetGenerateTree() [1/3] void CClustalOmegaToolParams::SetGenerateTree ( bool  value ) inline ◆ SetGenerateTree() [2/3] void CClustalwToolParams::SetGenerateTree ( bool  value ) inline ◆ SetGenerateTree() [3/3] void CMuscleToolParams::SetGenerateTree ( bool  value ) inline ◆ SetGeneticCode() void CBLASTSearchParamsPanel::SetGeneticCode ( wxString  value ) inline ◆ SetGenomicSeq() ◆ SetId() void CBLAST_Dlg_Item::SetId ( const wxTreeItemId &  id ) inline ◆ SetInput() void CNetBLASTLoadOptionPanel::SetInput ( const string &  input ) ◆ SetInputObjects() ◆ SetJobTitle() [1/2] void CBLASTSearchParamsPanel::SetJobTitle ( wxString  value ) inline ◆ SetJobTitle() [2/2] void CNGAlignParams::SetJobTitle ( wxString  value ) inline ◆ SetKalignPath() void CKalignToolParams::SetKalignPath ( wxString  value ) inline ◆ SetLeafLabels() void CTreeBuilderParams::SetLeafLabels ( wxString  value ) inline ◆ SetLoadingOptions() [1/2] ◆ SetLoadingOptions() [2/2] ◆ SetLocalDBLoader() void CBLASTParams::SetLocalDBLoader ( bool  value ) inline ◆ SetLocalNucDB() void CBLASTParams::SetLocalNucDB ( const string &  value ) inline ◆ SetLocalProtDB() void CBLASTParams::SetLocalProtDB ( const string &  value ) inline ◆ SetMafftPath() void CMafftToolParams::SetMafftPath ( wxString  value ) inline ◆ SetMatchCost() void CNeedlemanWunschToolParams::SetMatchCost ( int  value ) inline ◆ SetMaxGenomicExtent() void CSplignParams::SetMaxGenomicExtent ( long  value ) inline ◆ SetMaxIntron() void CSplignParams::SetMaxIntron ( long  value ) inline ◆ SetMaxSlop() void CFindOverlapParams::SetMaxSlop ( wxString  value ) inline ◆ SetMinCompIdentity() void CSplignParams::SetMinCompIdentity ( double  value ) inline ◆ SetMinExonIdentity() void CSplignParams::SetMinExonIdentity ( double  value ) inline ◆ SetMismatchCost() void CNeedlemanWunschToolParams::SetMismatchCost ( int  value ) inline ◆ SetMusclePath() void CMuscleToolParams::SetMusclePath ( wxString  value ) inline ◆ SetObject() ◆ SetObjects() [1/13] ◆ SetObjects() [2/13] ◆ SetObjects() [3/13] ◆ SetObjects() [4/13] ◆ SetObjects() [5/13] ◆ SetObjects() [6/13] ◆ SetObjects() [7/13] ◆ SetObjects() [8/13] ◆ SetObjects() [9/13] ◆ SetObjects() [10/13] ◆ SetObjects() [11/13] ◆ SetObjects() [12/13] ◆ SetObjects() [13/13] ◆ SetParams() [1/5] void CBLASTSearchParamsPanel::SetParams ( CBLASTParams *  params ) ◆ SetParams() [2/5] ◆ SetParams() [3/5] ◆ SetParams() [4/5] ◆ SetParams() [5/5] ◆ SetParentWindow() [1/4] void CBLASTToolManager::SetParentWindow ( wxWindow *  parent ) virtual ◆ SetParentWindow() [2/4] void CNetBLASTUILoadManager::SetParentWindow ( wxWindow *  parent ) virtual ◆ SetParentWindow() [3/4] void CPslLoadManager::SetParentWindow ( wxWindow *  parent ) virtual ◆ SetParentWindow() [4/4] void CTextAlignLoaderManager::SetParentWindow ( wxWindow *  parent ) virtual ◆ SetPolyADetect() void CSplignParams::SetPolyADetect ( bool  value ) inline ◆ SetPrevPage() virtual void CTextAlignLoaderManager::SetPrevPage ( IWizardPage *  ) inlinevirtual ◆ SetQueries() [1/2] ◆ SetQueries() [2/2] ◆ SetQuietFlag() [1/2] void CKalignToolParams::SetQuietFlag ( bool  value ) inline ◆ SetQuietFlag() [2/2] void CMafftToolParams::SetQuietFlag ( bool  value ) inline ◆ SetRegistryPath() [1/28] void CBLASTToolManager::SetRegistryPath ( const string &  path ) virtual ◆ SetRegistryPath() [2/28] void CCleanupAlignmentsParamsPanel::SetRegistryPath ( const string &  reg_path ) virtual ◆ SetRegistryPath() [3/28] virtual void CClustalOmegaToolParams::SetRegistryPath ( const string &  path ) inlinevirtual ◆ SetRegistryPath() [4/28] virtual void CClustalwToolParams::SetRegistryPath ( const string &  path ) inlinevirtual ◆ SetRegistryPath() [5/28] virtual void CFindOverlapParams::SetRegistryPath ( const string &  path ) inlinevirtual ◆ SetRegistryPath() [6/28] void CGroupAlignmentsParamsPanel::SetRegistryPath ( const string &  reg_path ) virtual ◆ SetRegistryPath() [7/28] virtual void CKalignToolParams::SetRegistryPath ( const string &  path ) inlinevirtual ◆ SetRegistryPath() [8/28] virtual void CMafftToolParams::SetRegistryPath ( const string &  path ) inlinevirtual ◆ SetRegistryPath() [9/28] void CMergeAlignmentsParamsPanel::SetRegistryPath ( const string &  reg_path ) virtual ◆ SetRegistryPath() [10/28] virtual void CMuscleToolParams::SetRegistryPath ( const string &  path ) inlinevirtual ◆ SetRegistryPath() [11/28] virtual void CNeedlemanWunschToolParams::SetRegistryPath ( const string &  path ) inlinevirtual ◆ SetRegistryPath() [12/28] void CNetBLASTUIDataSource::SetRegistryPath ( const string &  path ) virtual ◆ SetRegistryPath() [13/28] void CNetBLASTUILoadManager::SetRegistryPath ( const string &  path ) virtual ◆ SetRegistryPath() [14/28] virtual void CNGAlignParams::SetRegistryPath ( const string &  path ) inlinevirtual ◆ SetRegistryPath() [15/28] void CSplignPanel::SetRegistryPath ( const string &  reg_path ) virtual ◆ SetRegistryPath() [16/28] virtual void CSplignParams::SetRegistryPath ( const string &  path ) inlinevirtual ◆ SetRegistryPath() [17/28] virtual void CTaxTreeToolParams::SetRegistryPath ( const string &  path ) inlinevirtual ◆ SetRegistryPath() [18/28] virtual void CTreeBuilderParams::SetRegistryPath ( const string &  path ) inlinevirtual ◆ SetRegistryPath() [19/28] void CMuscleToolPanel::SetRegistryPath ( const string &  reg_path ) virtual ◆ SetRegistryPath() [20/28] void CPslLoadManager::SetRegistryPath ( const string &  path ) virtual ◆ SetRegistryPath() [21/28] void CTaxTreeToolPanel::SetRegistryPath ( const string &  reg_path ) virtual ◆ SetRegistryPath() [22/28] void CTextAlignLoaderManager::SetRegistryPath ( const string &  path ) virtual ◆ SetRegistryPath() [23/28] void CAlignSpanView::SetRegistryPath ( const string &  reg_path ) virtual ◆ SetRegistryPath() [24/28] void SCleanupAlignmentsParams::SetRegistryPath ( const string &  reg_path ) virtual ◆ SetRegistryPath() [25/28] void SGroupAlignmentsParams::SetRegistryPath ( const string &  reg_path ) virtual ◆ SetRegistryPath() [26/28] void SMergeAlignmentsParams::SetRegistryPath ( const string &  reg_path ) virtual ◆ SetRegistryPath() [27/28] void CMultiAlignView::SetRegistryPath ( const string &  reg_path ) virtual ◆ SetRegistryPath() [28/28] void CPhyTreeView::SetRegistryPath ( const string &  reg_path ) virtual ◆ SetRetrieved() void CNetBlastDMSearchFormPanel::SetRetrieved ( bool  value ) inline ◆ SetRIDs() ◆ SetScoringMethod() void CMuscleToolParams::SetScoringMethod ( int  value ) inline ◆ SetSearchValue() void CNetBlastDMSearchFormPanel::SetSearchValue ( wxString  value ) inline ◆ SetSecondSeqFreeEnds() void CNeedlemanWunschToolParams::SetSecondSeqFreeEnds ( int  value ) inline ◆ SetSelection() ◆ SetSeq1() ◆ SetSeq2() ◆ SetServiceLocator() [1/6] void CNetBLAST_DMSearchTool::SetServiceLocator ( IServiceLocator *  locator ) virtual ◆ SetServiceLocator() [2/6] void CNetBLASTUIDataSource::SetServiceLocator ( IServiceLocator *  locator ) virtual ◆ SetServiceLocator() [3/6] void CBLASTToolManager::SetServiceLocator ( IServiceLocator *  srv_locator ) virtual ◆ SetServiceLocator() [4/6] void CNetBLASTUILoadManager::SetServiceLocator ( IServiceLocator *  srv_locator ) virtual ◆ SetServiceLocator() [5/6] ◆ SetServiceLocator() [6/6] void CTextAlignLoaderManager::SetServiceLocator ( IServiceLocator *  srv_locator ) virtual ◆ SetSubject() [1/2] ◆ SetSubject() [2/2] ◆ SetSubjectType() void CBLASTParams::SetSubjectType ( ESubjectType  subjectType ) inline ◆ SetSubmitted() void CNetBlastDMSearchFormPanel::SetSubmitted ( bool  value ) inline ◆ SetThreshold() void CBLASTSearchParamsPanel::SetThreshold ( long  value ) inline ◆ SetToolName() void CBLAST_DB_Dialog::SetToolName ( const string &  tool ) ◆ Setup() ◆ SetVisible() void CBLAST_Dlg_Item::SetVisible ( bool  visible ) inline ◆ SetWM_Dir() void CBLASTParams::SetWM_Dir ( const string &  wm_dir_path ) inline ◆ SetWMDir() void CNGAlignParams::SetWMDir ( string  value ) inline ◆ SetWMTaxId() void CNGAlignParams::SetWMTaxId ( int  value ) inline ◆ SetWordSize() [1/2] void CBLASTSearchParamsPanel::SetWordSize ( long  value ) inline ◆ SetWordSize() [2/2] void CNGAlignParams::SetWordSize ( long  value ) inline ◆ SetWorkbench() void CMPCrossAlignView::SetWorkbench ( IWorkbench *  workbench ) virtual ◆ SGeneCdsmRnaFeats() ◆ SGroupAlignmentsParams() SGroupAlignmentsParams::SGroupAlignmentsParams ( ) ◆ ShowToolTips() [1/14] ◆ ShowToolTips() [2/14] bool CBLASTSearchOptionsPanel::ShowToolTips ( ) static ◆ ShowToolTips() [3/14] bool CBLASTSearchParamsPanel::ShowToolTips ( ) static ◆ ShowToolTips() [4/14] ◆ ShowToolTips() [5/14] ◆ ShowToolTips() [6/14] ◆ ShowToolTips() [7/14] ◆ ShowToolTips() [8/14] ◆ ShowToolTips() [9/14] ◆ ShowToolTips() [10/14] ◆ ShowToolTips() [11/14] ◆ ShowToolTips() [12/14] bool CMuscleToolPanel::ShowToolTips ( ) static ◆ ShowToolTips() [13/14] ◆ ShowToolTips() [14/14] ◆ SMergeAlignmentsParams() SMergeAlignmentsParams::SMergeAlignmentsParams ( ) ◆ SProgParams() [1/2] ◆ SProgParams() [2/2] ◆ StandaloneRequested() void CBLASTParams::StandaloneRequested ( bool  req ) inline ◆ StartMonitoringTask() void CNetBLASTUIDataSource::StartMonitoringTask ( TJobDescrVec &  descriptors ) ◆ StartRetrievingTask() void CNetBLASTUIDataSource::StartRetrievingTask ( TJobDescrVec &  descriptors ) ◆ Submit() void CNetBlastJobDescriptor::Submit ( objects::CBioseq_set &  seq_set )

Definition at line 279 of file net_blast_job_descr.cpp.

References _ASSERT, CNetBlastJobDescriptor::eInitial, CNetBlastJobDescriptor::eSubmitted, eUnknown, CNetBlastJobDescriptor::m_Mutex, CNetBlastJobDescriptor::m_RemoteBlast, CNetBlastJobDescriptor::m_RID, CNetBlastJobDescriptor::m_State, CNetBlastJobDescriptor::m_SubmitTime, NCBI_THROW, and CNetBlastJobDescriptor::x_NotifyDataSource().

◆ TaxonsLoaded() void CBLASTSearchParamsPanel::TaxonsLoaded ( bool  local ) virtual ◆ TestInputObjects() [1/7] ◆ TestInputObjects() [2/7] ◆ TestInputObjects() [3/7] ◆ TestInputObjects() [4/7] ◆ TestInputObjects() [5/7] ◆ TestInputObjects() [6/7] ◆ TestInputObjects() [7/7] ◆ ToArgs() CArgs * CBLASTParams::ToArgs ( vector< string > &  argv ) const

Definition at line 1041 of file blast_search_params.cpp.

References eBlastn, eBlastp, eBlastx, eDiscMegablast, eMegablast, EProgramToTaskName(), eTblastn, eTblastx, eUnknown, CBLASTParams::GetCurrProgram(), NCBI_THROW, CRef< C, Locker >::Reset(), and CBLASTParams::ToArgVec().

◆ ToArgVec() vector< string > & CBLASTParams::ToArgVec ( vector< string > &  arg_vec ) const

Definition at line 952 of file blast_search_params.cpp.

References NStr::DoubleToString(), ERR_POST, Error(), CBLASTParams::GetAdvancedParams(), CSystemInfo::GetCpuCount(), CBLASTParams::GetCurrParams(), CBLASTParams::GetCurrProgram(), CBLASTParams::GetRepeatDb(), CBLASTParams::GetWmDir(), NStr::IntToString(), CBLASTParams::IsNucInput(), kArgDbGeneticCode, kArgDustFiltering, kArgEvalue, kArgFilteringDb, kArgNumThreads, kArgQueryGeneticCode, kArgSegFiltering, kArgUseLCaseMasking, kArgWindowMaskerTaxId, kArgWordScoreThreshold, kArgWordSize, kDfltArgApplyFiltering, CBLASTParams::SProgParams::m_DbGeneticCode, CBLASTParams::SProgParams::m_eValue, CBLASTParams::SProgParams::m_FilterLowComplex, CBLASTParams::SProgParams::m_MaskLowercase, CBLASTParams::SProgParams::m_MaskRepeats, CBLASTParams::SProgParams::m_QueryGeneticCode, CBLASTParams::SProgParams::m_RepeatLib, CBLASTParams::SProgParams::m_Threshold, CBLASTParams::SProgParams::m_WM_TaxId, CBLASTParams::SProgParams::m_WordSize, CBLASTParams::NeedsDbGeneticCode(), CBLASTParams::NeedsQueryGeneticCode(), CBLASTParams::NeedsThreshold(), NStr::Split(), CBLASTParams::UseDustFilter(), and Warning().

Referenced by CBLASTParams::ToArgs(), CBLASTParams::ToArgVecBlastOptions(), and CBLASTParams::ToBlastOptions().

◆ ToArgVecBlastOptions() CRef< blast::CBlastOptionsHandle > CBLASTParams::ToArgVecBlastOptions ( vector< string > &  arg_vec, bool  local = true  ) const

Definition at line 751 of file blast_search_params.cpp.

References CBlastOptionsFactory::Create(), eBlastn, eBlastp, eBlastx, eDiscMegablast, CBlastOptions::eLocal, eMegablast, EProgramToTaskName(), CBlastOptions::eRemote, eTblastn, eTblastx, eUnknown, CBLASTParams::GetCurrProgram(), kTask, local, NCBI_THROW, CRef< C, Locker >::Reset(), and CBLASTParams::ToArgVec().

Referenced by CBLASTSeqToolJob::x_CreateProjectItems().

◆ ToBlastOptions() CRef< blast::CBlastOptionsHandle > CBLASTParams::ToBlastOptions ( bool  local = false ) const

Definition at line 820 of file blast_search_params.cpp.

References CBlastOptionsFactory::Create(), eBlastn, eBlastp, eBlastx, eDiscMegablast, CBlastOptions::eLocal, eMegablast, EProgramToTaskName(), CBlastOptions::eRemote, eTblastn, eTblastx, eUnknown, CBLASTParams::GetCurrProgram(), local, NCBI_THROW, CRef< C, Locker >::Reset(), and CBLASTParams::ToArgVec().

Referenced by CNetBlastJobDescriptor::Init(), and CBLASTToolManager::x_ValidateParams().

◆ ToString() string CNetBLAST_DMSearchQuery::ToString ( ) const virtual ◆ ToUserObject() [1/2]

Definition at line 503 of file blast_search_params.cpp.

References CUser_object::AddField(), CMRUList< T >::GetItems(), CBLASTParams::GetProgramLabel(), ITERATE, kAdvParamsTag, kBLASTParamsTag, kEntrezQueryTag, kJobTitleTag, kLocalDBLoader, kLocalNucDB, kLocalProtDB, kNucDBTag, kNucMRUDBsTag, kNucProgTag, kProtDBTag, kProtMRUDBsTag, kProtProgTag, kSubjectType, CBLASTParams::m_AdvancedParams, CBLASTParams::m_EntrezQuery, CBLASTParams::m_JobTitle, CBLASTParams::m_LocalDBLoader, CBLASTParams::m_LocalNucDB, CBLASTParams::m_LocalProtDB, CBLASTParams::m_NucDatabase, CBLASTParams::m_NucMRUDatabases, CBLASTParams::m_NucProgram, CBLASTParams::m_ProgToParams, CBLASTParams::m_ProtDatabase, CBLASTParams::m_ProtMRUDatabases, CBLASTParams::m_ProtProgram, CBLASTParams::m_SubjectType, CRef< C, Locker >::Release(), CUser_object_Base::SetType(), val, and CBLASTParams::x_ToUserObject().

Referenced by CBLASTToolManager::SaveSettings().

◆ ToUserObject() [2/2] CUser_object * CNetBlastJobDescriptor::ToUserObject ( ) const

Definition at line 393 of file net_blast_job_descr.cpp.

References CUser_object::AddField(), CTime::AsString(), kBLASTJobTag, kDescrTag, kErrorsTag, kRIDTag, kStateTag, kSubmitTimeTag, kTitleTag, CNetBlastJobDescriptor::m_Description, CNetBlastJobDescriptor::m_Errors, CNetBlastJobDescriptor::m_JobTitle, CNetBlastJobDescriptor::m_RID, CNetBlastJobDescriptor::m_State, CNetBlastJobDescriptor::m_SubmitTime, CRef< C, Locker >::Release(), and CUser_object_Base::SetType().

Referenced by CNetBLASTUIDataSource::x_SaveJobDescriptors().

◆ TransferDataFromWindow() [1/11] bool CBLASTSearchOptionsPanel::TransferDataFromWindow ( )

Definition at line 453 of file blast_search_options_panel.cpp.

References CBLASTParams::eLocalDB, CBLASTParams::eNCBIDB, CBLASTParams::GetCurrDatabase(), CBLASTParams::GetCurrProgram(), CBLASTParams::GetEntrezQuery(), CBLASTDatabases::GetInstance(), CBLASTParams::GetProgramByLabel(), CObjectListWidget::GetSelection(), CBLASTParams::GetSeqLocs(), CBLASTParams::GetSubjectType(), CBLASTParams::GetSubjSeqLocs(), CBLASTParams::IsNucInput(), CBLASTParams::IsSubjNucInput(), CBLASTSearchOptionsPanel::m_DatabaseCombo, CBLASTSearchOptionsPanel::m_LocalDBCtrl, CBLASTSearchOptionsPanel::m_NucRadio, CBLASTSearchOptionsPanel::m_Params, CBLASTSearchOptionsPanel::m_ProgramCombo, CBLASTSearchOptionsPanel::m_QueryCombo, CBLASTSearchOptionsPanel::m_QueryListCtrl, CBLASTSearchOptionsPanel::m_SubjectListCtrl, CBLASTParams::SetLocalNucDB(), CBLASTParams::SetLocalProtDB(), ToStdString(), CLBLASTParamsPanel::ValidateLocalDatabase(), and wxT.

Referenced by CBLASTToolManager::DoTransition().

◆ TransferDataFromWindow() [2/11] bool CBLASTSearchParamsPanel::TransferDataFromWindow ( )

Definition at line 521 of file blast_search_params_panel.cpp.

References CBLASTParams::eSequences, CBLASTParams::FindCompartments(), CBLASTParams::GetAdvancedParams(), CBLASTParams::GetCurrParams(), CBLASTParams::GetCurrProgram(), CBLASTParams::GetGeneticCodeByLabel(), CWinMaskerFileStorage::GetInstance(), CBLASTParams::GetJobTitle(), CWinMaskerFileStorage::GetPath(), CBLASTParams::GetSubjectType(), int, CBLASTSearchParamsPanel::m_AdvParams, CBLASTSearchParamsPanel::m_chbStandalone, CBLASTSearchParamsPanel::m_CompartCheck, CBLASTParams::SProgParams::m_DbGeneticCode, CBLASTSearchParamsPanel::m_DbGeneticCode, CBLASTParams::SProgParams::m_eValue, CBLASTSearchParamsPanel::m_eValue, CBLASTParams::SProgParams::m_FilterLowComplex, CBLASTSearchParamsPanel::m_FilterLowComplex, CBLASTSearchParamsPanel::m_JobTitle, CBLASTSearchParamsPanel::m_Local, CBLASTSearchParamsPanel::m_MaskLCRegions, CBLASTParams::SProgParams::m_MaskLowercase, CBLASTParams::SProgParams::m_MaskRepeats, CBLASTSearchParamsPanel::m_MaskRepeats, CBLASTSearchParamsPanel::m_Params, CBLASTParams::SProgParams::m_QueryGeneticCode, CBLASTSearchParamsPanel::m_QueryGeneticCode, CBLASTParams::SProgParams::m_RepeatLib, CBLASTSearchParamsPanel::m_RepeatType, CBLASTParams::SProgParams::m_Threshold, CBLASTSearchParamsPanel::m_Threshold, CBLASTParams::SProgParams::m_WM_TaxId, CBLASTSearchParamsPanel::m_WMTaxIds, CBLASTParams::SProgParams::m_WordSize, CBLASTSearchParamsPanel::m_WordSize, CBLASTParams::NeedsDbGeneticCode(), CBLASTParams::NeedsQueryGeneticCode(), CBLASTParams::NeedsThreshold(), CBLASTParams::SetWM_Dir(), CBLASTParams::StandaloneRequested(), and ToStdString().

Referenced by CBLASTToolManager::DoTransition().

◆ TransferDataFromWindow() [3/11] bool CCleanupAlignmentsParamsPanel::TransferDataFromWindow ( )

Definition at line 336 of file cleanup_alignments_params_panel.cpp.

References SCleanupAlignmentsParams::eAlignmentManager, SCleanupAlignmentsParams::eHitFilter, CObjectListWidget::GetSelection(), SCleanupAlignmentsParams::m_Algo, CCleanupAlignmentsParamsPanel::m_AlgoSelector, SCleanupAlignmentsParams::m_Alignments, SCleanupAlignmentsParams::m_AlnMgr_FillUnaligned, CCleanupAlignmentsParamsPanel::m_AlnMgr_FillUnaligned, SCleanupAlignmentsParams::m_AlnMgr_PreserveRows, CCleanupAlignmentsParamsPanel::m_AlnMgr_PreserveRows, SCleanupAlignmentsParams::m_AlnMgr_Sort, CCleanupAlignmentsParamsPanel::m_AlnMgr_Sort, SCleanupAlignmentsParams::m_AlnMgr_Transloc, CCleanupAlignmentsParamsPanel::m_AlnMgr_Transloc, SCleanupAlignmentsParams::m_HitFilter_MinIdentity, CCleanupAlignmentsParamsPanel::m_HitFilter_MinIdentity, SCleanupAlignmentsParams::m_HitFilter_MinLength, CCleanupAlignmentsParamsPanel::m_HitFilter_MinLength, CCleanupAlignmentsParamsPanel::m_ObjectList, CCleanupAlignmentsParamsPanel::m_Params, NStr::StringToDouble(), NStr::StringToInt(), and ToStdString().

◆ TransferDataFromWindow() [4/11] bool CFindOverlapPanel::TransferDataFromWindow ( ) virtual ◆ TransferDataFromWindow() [5/11] bool CGroupAlignmentsParamsPanel::TransferDataFromWindow ( )

Definition at line 347 of file group_alignments_params_panel.cpp.

References CObjectListWidget::GetSelection(), SGroupAlignmentsParams::m_Alignments, SGroupAlignmentsParams::m_GroupByEST, CGroupAlignmentsParamsPanel::m_GroupByEST, SGroupAlignmentsParams::m_GroupByHTGS, CGroupAlignmentsParamsPanel::m_GroupByHTGS, SGroupAlignmentsParams::m_GroupByLikeTaxId, CGroupAlignmentsParamsPanel::m_GroupByLikeTaxId, SGroupAlignmentsParams::m_GroupByPatent, CGroupAlignmentsParamsPanel::m_GroupByPatent, SGroupAlignmentsParams::m_GroupByPredictedRefSeq, CGroupAlignmentsParamsPanel::m_GroupByPredictedRefSeq, SGroupAlignmentsParams::m_GroupByRefSeq, CGroupAlignmentsParamsPanel::m_GroupByRefSeq, SGroupAlignmentsParams::m_GroupBySeqId, CGroupAlignmentsParamsPanel::m_GroupBySeqId, SGroupAlignmentsParams::m_GroupByStrand, CGroupAlignmentsParamsPanel::m_GroupByStrand, SGroupAlignmentsParams::m_GroupByTaxId, CGroupAlignmentsParamsPanel::m_GroupByTaxId, SGroupAlignmentsParams::m_GroupByWGS, CGroupAlignmentsParamsPanel::m_GroupByWGS, CGroupAlignmentsParamsPanel::m_ObjectList, and CGroupAlignmentsParamsPanel::m_Params.

◆ TransferDataFromWindow() [6/11] bool CMergeAlignmentsParamsPanel::TransferDataFromWindow ( )

Definition at line 261 of file merge_alignments_params_panel.cpp.

References CAlnUserOptions::eBothDirections, CAlnUserOptions::eMergeAllSeqs, CAlnUserOptions::eQuerySeqMergeOnly, CAlnUserOptions::eReverse, CAlnUserOptions::fSkipSortByScore, CAlnUserOptions::fTruncateOverlaps, CObjectListWidget::GetSelection(), SMergeAlignmentsParams::m_Alignments, CMergeAlignmentsParamsPanel::m_AssumeNegStrand, SMergeAlignmentsParams::m_Direction, SMergeAlignmentsParams::m_FillUnaligned, CMergeAlignmentsParamsPanel::m_FillUnaligned, SMergeAlignmentsParams::m_MergeAlgo, SMergeAlignmentsParams::m_MergeFlags, CMergeAlignmentsParamsPanel::m_MergeQuerySeqOnly, CMergeAlignmentsParamsPanel::m_ObjectListCtrl, CMergeAlignmentsParamsPanel::m_Params, CMergeAlignmentsParamsPanel::m_SortInput, and CMergeAlignmentsParamsPanel::m_TruncateOverlap.

◆ TransferDataFromWindow() [7/11] bool CSplignPanel::TransferDataFromWindow ( ) virtual ◆ TransferDataFromWindow() [8/11] bool CTreeBuilderPanel::TransferDataFromWindow ( ) virtual

Definition at line 209 of file tree_builder_panel.cpp.

References CObjectListWidget::GetSelection(), CTreeBuilderPanel::m_data, CTreeBuilderPanel::m_pConstruct, CTreeBuilderPanel::m_pDistance, CTreeBuilderPanel::m_pLabels, CTreeBuilderPanel::m_Seq1List, CTreeBuilderParams::SetConstructMethod(), CTreeBuilderParams::SetDistanceMethod(), CTreeBuilderParams::SetLeafLabels(), CTreeBuilderParams::SetObject(), and wxT.

◆ TransferDataFromWindow() [9/11] bool CMuscleToolPanel::TransferDataFromWindow ( ) virtual ◆ TransferDataFromWindow() [10/11] bool CNGAlignPanel::TransferDataFromWindow ( ) virtual ◆ TransferDataFromWindow() [11/11] bool CTaxTreeToolPanel::TransferDataFromWindow ( ) virtual ◆ TransferDataToWindow() [1/8] bool CBLASTSearchOptionsPanel::TransferDataToWindow ( )

Definition at line 428 of file blast_search_options_panel.cpp.

References CBLASTParams::eLocalDB, CBLASTParams::eNCBIDB, CBLASTParams::eSequences, CBLASTParams::GetEntrezQuery(), CBLASTParams::GetLocalDBLoader(), CBLASTParams::GetSubjectType(), CBLASTParams::IsNucInput(), CBLASTSearchOptionsPanel::m_LocalDBLoaderCtrl, CBLASTSearchOptionsPanel::m_NucRadio, CBLASTSearchOptionsPanel::m_Params, CBLASTSearchOptionsPanel::m_ProtRadio, CBLASTSearchOptionsPanel::m_QueryCombo, CBLASTSearchOptionsPanel::m_SubjectTypeLDBCtrl, CBLASTSearchOptionsPanel::m_SubjectTypeNCBICtrl, CBLASTSearchOptionsPanel::m_SubjectTypeSeqsCtrl, query, ToWxString(), CBLASTSearchOptionsPanel::x_CheckDBLoaded(), CBLASTSearchOptionsPanel::x_OnInputTypeChanged(), and CBLASTSearchOptionsPanel::x_UpdateSubjectType().

Referenced by CBLASTToolManager::DoTransition(), and CBLASTSearchOptionsPanel::RestoreDefaults().

◆ TransferDataToWindow() [2/8] bool CBLASTSearchParamsPanel::TransferDataToWindow ( )

Definition at line 413 of file blast_search_params_panel.cpp.

References CBLASTParams::eNCBIDB, CBLASTParams::eSequences, CBLASTParams::GetAdvancedParams(), CBLASTParams::GetCurrParams(), CBLASTParams::GetCurrProgram(), CBLASTParams::GetGeneticCodeLabel(), CBLASTParams::GetJobTitle(), CBLASTParams::GetSubjectType(), CBLASTParams::IsCompartmentsRequested(), CBLASTParams::IsNucInput(), CBLASTParams::IsStandaloneRequested(), CBLASTSearchParamsPanel::m_AdvParams, CBLASTSearchParamsPanel::m_chbStandalone, CBLASTSearchParamsPanel::m_CompartCheck, CBLASTParams::SProgParams::m_DbGeneticCode, CBLASTSearchParamsPanel::m_DbGeneticCode, CBLASTParams::SProgParams::m_eValue, CBLASTSearchParamsPanel::m_eValue, CBLASTParams::SProgParams::m_FilterLowComplex, CBLASTSearchParamsPanel::m_FilterLowComplex, CBLASTSearchParamsPanel::m_JobTitle, CBLASTSearchParamsPanel::m_Local, CBLASTSearchParamsPanel::m_MaskLCRegions, CBLASTParams::SProgParams::m_MaskLowercase, CBLASTParams::SProgParams::m_MaskRepeats, CBLASTSearchParamsPanel::m_MaskRepeats, CBLASTSearchParamsPanel::m_Params, CBLASTParams::SProgParams::m_QueryGeneticCode, CBLASTSearchParamsPanel::m_QueryGeneticCode, CBLASTParams::SProgParams::m_RepeatLib, CBLASTSearchParamsPanel::m_RepeatType, CBLASTParams::SProgParams::m_Threshold, CBLASTSearchParamsPanel::m_Threshold, CBLASTParams::SProgParams::m_WordSize, CBLASTSearchParamsPanel::m_WordSize, CBLASTParams::NeedsDbGeneticCode(), CBLASTParams::NeedsQueryGeneticCode(), CBLASTParams::NeedsThreshold(), ToWxString(), wxT, CBLASTSearchParamsPanel::x_HideShowInputs(), and CBLASTSearchParamsPanel::x_InitTaxons().

Referenced by CBLASTToolManager::DoTransition(), and CBLASTSearchParamsPanel::RestoreDefaults().

◆ TransferDataToWindow() [3/8] bool CCleanupAlignmentsParamsPanel::TransferDataToWindow ( )

Definition at line 303 of file cleanup_alignments_params_panel.cpp.

References NStr::DoubleToString(), SCleanupAlignmentsParams::eAlignmentManager, SCleanupAlignmentsParams::eHitFilter, SCleanupAlignmentsParams::m_Algo, CCleanupAlignmentsParamsPanel::m_AlgoSelector, SCleanupAlignmentsParams::m_AlnMgr_FillUnaligned, CCleanupAlignmentsParamsPanel::m_AlnMgr_FillUnaligned, SCleanupAlignmentsParams::m_AlnMgr_PreserveRows, CCleanupAlignmentsParamsPanel::m_AlnMgr_PreserveRows, SCleanupAlignmentsParams::m_AlnMgr_Sort, CCleanupAlignmentsParamsPanel::m_AlnMgr_Sort, SCleanupAlignmentsParams::m_HitFilter_MinIdentity, CCleanupAlignmentsParamsPanel::m_HitFilter_MinIdentity, SCleanupAlignmentsParams::m_HitFilter_MinLength, CCleanupAlignmentsParamsPanel::m_HitFilter_MinLength, CCleanupAlignmentsParamsPanel::m_InputListDirty, CCleanupAlignmentsParamsPanel::m_InputObjects, CCleanupAlignmentsParamsPanel::m_ObjectList, CCleanupAlignmentsParamsPanel::m_Params, CwxTableListCtrl::SelectAll(), CObjectListWidget::SetObjects(), ToWxString(), and CCleanupAlignmentsParamsPanel::x_AdjustToAlgoSelector().

Referenced by CCleanupAlignmentsParamsPanel::RestoreDefaults().

◆ TransferDataToWindow() [4/8] bool CFindOverlapPanel::TransferDataToWindow ( ) virtual ◆ TransferDataToWindow() [5/8] bool CGroupAlignmentsParamsPanel::TransferDataToWindow ( )

Definition at line 324 of file group_alignments_params_panel.cpp.

References SGroupAlignmentsParams::m_GroupByEST, CGroupAlignmentsParamsPanel::m_GroupByEST, SGroupAlignmentsParams::m_GroupByHTGS, CGroupAlignmentsParamsPanel::m_GroupByHTGS, SGroupAlignmentsParams::m_GroupByLikeTaxId, CGroupAlignmentsParamsPanel::m_GroupByLikeTaxId, SGroupAlignmentsParams::m_GroupByPatent, CGroupAlignmentsParamsPanel::m_GroupByPatent, SGroupAlignmentsParams::m_GroupByPredictedRefSeq, CGroupAlignmentsParamsPanel::m_GroupByPredictedRefSeq, SGroupAlignmentsParams::m_GroupByRefSeq, CGroupAlignmentsParamsPanel::m_GroupByRefSeq, SGroupAlignmentsParams::m_GroupBySeqId, CGroupAlignmentsParamsPanel::m_GroupBySeqId, SGroupAlignmentsParams::m_GroupByStrand, CGroupAlignmentsParamsPanel::m_GroupByStrand, SGroupAlignmentsParams::m_GroupByTaxId, CGroupAlignmentsParamsPanel::m_GroupByTaxId, SGroupAlignmentsParams::m_GroupByWGS, CGroupAlignmentsParamsPanel::m_GroupByWGS, CGroupAlignmentsParamsPanel::m_InputListDirty, CGroupAlignmentsParamsPanel::m_InputObjects, CGroupAlignmentsParamsPanel::m_ObjectList, CGroupAlignmentsParamsPanel::m_Params, CwxTableListCtrl::SelectAll(), and CObjectListWidget::SetObjects().

Referenced by CGroupAlignmentsParamsPanel::RestoreDefaults().

◆ TransferDataToWindow() [6/8] bool CMergeAlignmentsParamsPanel::TransferDataToWindow ( )

Definition at line 243 of file merge_alignments_params_panel.cpp.

References CAlnUserOptions::eQuerySeqMergeOnly, CAlnUserOptions::eReverse, CAlnUserOptions::fSkipSortByScore, CAlnUserOptions::fTruncateOverlaps, CMergeAlignmentsParamsPanel::m_AssumeNegStrand, SMergeAlignmentsParams::m_Direction, SMergeAlignmentsParams::m_FillUnaligned, CMergeAlignmentsParamsPanel::m_FillUnaligned, CMergeAlignmentsParamsPanel::m_InputListDirty, CMergeAlignmentsParamsPanel::m_InputObjects, SMergeAlignmentsParams::m_MergeAlgo, SMergeAlignmentsParams::m_MergeFlags, CMergeAlignmentsParamsPanel::m_MergeQuerySeqOnly, CMergeAlignmentsParamsPanel::m_ObjectListCtrl, CMergeAlignmentsParamsPanel::m_Params, CMergeAlignmentsParamsPanel::m_SortInput, CMergeAlignmentsParamsPanel::m_TruncateOverlap, CwxTableListCtrl::SelectAll(), and CObjectListWidget::SetObjects().

Referenced by CMergeAlignmentsParamsPanel::RestoreDefaults().

◆ TransferDataToWindow() [7/8] bool CNetBlastDMSearchFormPanel::TransferDataToWindow ( ) ◆ TransferDataToWindow() [8/8] bool CTreeBuilderPanel::TransferDataToWindow ( ) virtual ◆ Update() void CNetBLAST_DMSearchForm::Update ( void  ) virtual ◆ UpdateContexts() void CNetBLAST_DMSearchForm::UpdateContexts ( ) virtual ◆ UseDustFilter() ◆ Validate() CConstRef< CObject > CMolTypeValidator::Validate ( const objects::CSeq_id &  id, objects::CScope &  scope, wxString &  errMessage  ) virtual

Implements IObjectListAccValidator.

Definition at line 73 of file splign_panel.cpp.

References CSeqdesc_Base::e_Molinfo, CMolInfo_Base::eBiomol_genomic, CMolInfo_Base::eBiomol_peptide, CMolInfo_Base::eBiomol_unknown, CRelation::fConvert_NoExpensive, CObjectConverter::FindRelations(), CMolInfo_Base::GetBiomol(), CSeq_loc::GetId(), CSeqdesc_Base::GetMolinfo(), CException::GetMsg(), CBioseq_Handle::IsAa(), CBioseq_Handle::IsNa(), ITERATE, CException::what(), and wxT.

◆ ValidateFilenames() [1/2] bool CPslLoadManager::ValidateFilenames ( const vector< wxString > &  filenames ) virtual ◆ ValidateFilenames() [2/2] bool CTextAlignLoaderManager::ValidateFilenames ( const vector< wxString > &  filenames ) virtual ◆ x_AddError() void CNetBlastSubmittingJob::x_AddError ( const string &  error ) protected ◆ x_AddProgramParams() ◆ x_AddTreeProjectItem()

Definition at line 315 of file msa_tool_job.cpp.

References CDataLoadingAppJob::AddProjectItem(), Error(), CException::GetMsg(), STreeNodeMapper::idmap, LOG_POST, CMSAToolJob::m_IdMap, CMSAToolJob::m_TmpTreeOut, MakeBioTreeContainer(), NON_CONST_ITERATE, ReadNewickTree(), CRef< C, Locker >::Reset(), CAnnotdesc_Base::SetComment(), CProjectItem_Base::SetDescr(), CBioTreeContainer_Base::SetFdict(), CProjectItem_Base::SetItem(), CProjectItem_Base::SetLabel(), CBioTreeContainer_Base::SetNodes(), CBioTreeContainer_Base::SetTreetype(), TreeDepthFirstTraverse(), and CException::what().

Referenced by CMSAToolJob::x_CreateProjectItems().

◆ x_AdjustToAlgoSelector() void CCleanupAlignmentsParamsPanel::x_AdjustToAlgoSelector ( ) private ◆ x_AreSelfAlignmentsOnly() bool CCleanupAlignmentsToolManager::x_AreSelfAlignmentsOnly ( ) const protected ◆ x_ArgsToBlastOptions() void CBLASTParams::x_ArgsToBlastOptions ( const string &  cmd_line, blast::CBlastOptions &  opts  ) const protected ◆ x_AssignIDsAndCrossLinkFeats() void CCreateGeneModelTask::x_AssignIDsAndCrossLinkFeats ( objects::CSeq_annot &  annot, const objects::CSeq_id_Handle &  idh, objects::CObject_id::TId  max_id  ) private ◆ x_AssignIDsAndUpdateGenes() CRef< CCmdComposite > CCreateGeneModelTask::x_AssignIDsAndUpdateGenes ( objects::CSeq_annot &  annot, const objects::CSeq_id_Handle &  idh, objects::CSeq_entry_Handle  seh  ) private

Definition at line 798 of file create_gene_model_tool_manager.cpp.

References CSerialObject::Assign(), cmd, NStr::CommonPrefixSize(), CSeqFeatData::eSubtype_mRNA, eWithAccessionVersion, NStr::FindNoCase(), GetAccessionForId(), CSeq_feat_Handle::GetAnnot(), CSeq_entry_Handle::GetEditHandle(), CSeq_feat_Base::GetId(), CSeq_feat_Handle::GetId(), CSeq_feat_Handle::GetOriginalSeq_feat(), CSeq_annot_Handle::GetParentEntry(), NStr::IsBlank(), CSeq_feat_Base::IsSetId(), CSeq_feat_Handle::IsSetId(), CCreateGeneModelTask::m_GeneModelMap, CCreateGeneModelTask::m_Params, SCreateGeneModelParams::m_PropagateLocalIds, CCreateGeneModelTask::m_Scope, NCBI_USER_THROW, NON_CONST_ITERATE, NPOS, CCreateGeneModelTask::s_AssignFeatureIds(), CCreateGeneModelTask::s_FeaturesHaveIDs(), CCreateGeneModelTask::s_FeaturesHaveXrefs(), CCreateGeneModelTask::s_FindHighestFeatId(), s_GetCDSformRNA(), NStr::StringToInt(), and CCreateGeneModelTask::x_GetUpdatedGeneCommand().

Referenced by CCreateGeneModelTask::x_GetCommand().

◆ x_AutoStartMonitoring() void CNetBLASTUIDataSource::x_AutoStartMonitoring ( ) protected ◆ x_BuildTreeItems()

Definition at line 377 of file blast_db_dialog.cpp.

References data, CBLAST_Dlg_Item::GetChildItems(), CBLAST_Dlg_Item::GetId(), CBLAST_Dlg_Item::GetLabel(), CBLAST_Dlg_Item::GetParent(), CBLAST_Dlg_Item::IsExpanded(), CBLAST_Dlg_Item::IsVisible(), label, CBLAST_DB_Dialog::m_TreeCtrl, NON_CONST_ITERATE, and CBLAST_Dlg_Item::SetId().

Referenced by CBLAST_DB_Dialog::x_CreateTreeItems().

◆ x_CheckDBLoaded() void CBLASTSearchOptionsPanel::x_CheckDBLoaded ( ) protected

Definition at line 796 of file blast_search_options_panel.cpp.

References CBLASTDatabases::eFailed, CBLASTDatabases::eInitial, CBLASTDatabases::eLoaded, CBLASTDatabases::eLoading, CBLASTParams::eNCBIDB, CBLASTDatabases::GetInstance(), CBLASTDatabases::GetState(), CBLASTParams::GetSubjectType(), CBLASTSearchOptionsPanel::ID_DBS_FAILED, CBLASTSearchOptionsPanel::ID_DBS_LOADING_PROGRESS, CBLASTSearchOptionsPanel::ID_DBS_LOADING_TEXT, CBLASTSearchOptionsPanel::ID_DBS_TRY_AGAIN, CBLASTSearchOptionsPanel::m_BrowseDBBtn, CBLASTSearchOptionsPanel::m_DatabaseCombo, CBLASTSearchOptionsPanel::m_DBLoadState, CBLASTSearchOptionsPanel::m_DBSizer, CBLASTSearchOptionsPanel::m_Params, CBLASTSearchOptionsPanel::m_Timer, and CBLASTSearchOptionsPanel::x_UpdateDBCombo().

Referenced by CBLASTSearchOptionsPanel::OnTimer(), CBLASTSearchOptionsPanel::OnTryAgain(), CBLASTSearchOptionsPanel::TransferDataToWindow(), and CBLASTSearchOptionsPanel::x_UpdateSubjectType().

◆ x_CreateBALSTPanelIfNeeded() void CNGAlignTool::x_CreateBALSTPanelIfNeeded ( ) protected ◆ x_CreateItems() void CBLAST_DB_Dialog::x_CreateItems ( ) protected

Definition at line 333 of file blast_db_dialog.cpp.

References CBLAST_Dlg_Item::AddChild(), CBLAST_Dlg_Item::GetChildByLabel(), CRef< C, Locker >::GetPointer(), i, ITERATE, label, CBLAST_DB_Dialog::m_CatItems, CBLAST_DB_Dialog::m_DbItems, CBLAST_DB_Dialog::m_DbMap, CBLAST_DB_Dialog::m_Root, n, NULL, CRef< C, Locker >::Reset(), and NStr::Split().

Referenced by CBLAST_DB_Dialog::OnInitDialog().

◆ x_CreateJob() ◆ x_CreateLoadingJob() [1/17] ◆ x_CreateLoadingJob() [2/17] ◆ x_CreateLoadingJob() [3/17] ◆ x_CreateLoadingJob() [4/17] ◆ x_CreateLoadingJob() [5/17] ◆ x_CreateLoadingJob() [6/17] ◆ x_CreateLoadingJob() [7/17] ◆ x_CreateLoadingJob() [8/17] ◆ x_CreateLoadingJob() [9/17] ◆ x_CreateLoadingJob() [10/17] ◆ x_CreateLoadingJob() [11/17] ◆ x_CreateLoadingJob() [12/17]

factory method for creating the job that executes the tool algorithm override in derived classes

Implements CAlgoToolManagerBase.

Definition at line 169 of file prosplign_tool.cpp.

References _ASSERT, copy(), CDebugDumpable::DebugDumpText(), CProSplignPanel::GetData(), CProSplignPanel::GetNucleotideSeqs(), CProSplignPanel::GetProteinSeq(), CProSplignTool::m_NAObjects, CProSplignTool::m_Panel, CProSplignTool::m_Params, CProSplignTool::m_ProteinObjects, and NON_CONST_ITERATE.

◆ x_CreateLoadingJob() [13/17] ◆ x_CreateLoadingJob() [14/17] ◆ x_CreateLoadingJob() [15/17] ◆ x_CreateLoadingJob() [16/17] ◆ x_CreateLoadingJob() [17/17] ◆ x_CreateMenuBarMenu() [1/7] void CAlignSpanView::x_CreateMenuBarMenu ( ) protectedvirtual ◆ x_CreateMenuBarMenu() [2/7] void CAnnotCompareView::x_CreateMenuBarMenu ( ) protectedvirtual ◆ x_CreateMenuBarMenu() [3/7] void CCrossAlignView::x_CreateMenuBarMenu ( ) protectedvirtual

initializes m_MenuBarMenu; override in derived classes

Reimplemented from CProjectViewBase.

Definition at line 83 of file cross_align_view.cpp.

References CUICommandRegistry::AppendMenuItem(), eCmdChooseSeq, eCmdZoomAllQuery, eCmdZoomAllSubject, eCmdZoomInQuery, eCmdZoomInSubject, eCmdZoomOutQuery, eCmdZoomOutSubject, IWorkbench::GetUICommandRegistry(), CProjectViewBase::m_MenuBarMenu, CProjectViewBase::m_Workbench, wxID_ANY, and wxT.

◆ x_CreateMenuBarMenu() [4/7] void CDotMatrixView::x_CreateMenuBarMenu ( ) protectedvirtual ◆ x_CreateMenuBarMenu() [5/7] void CMPCrossAlignView::x_CreateMenuBarMenu ( ) protectedvirtual ◆ x_CreateMenuBarMenu() [6/7] static void CMultiAlignView::x_CreateMenuBarMenu ( ) protectedvirtual ◆ x_CreateMenuBarMenu() [7/7] void CPhyTreeView::x_CreateMenuBarMenu ( ) protectedvirtual ◆ x_CreateOptionsPanelIfNeeded() void CBLASTToolManager::x_CreateOptionsPanelIfNeeded ( ) protectedvirtual

Definition at line 149 of file blast_tool_manager.cpp.

References CBLASTSearchOptionsPanel::Create(), CBLASTToolManager::GetBLASTDataSource(), CUIObject::GetLabel(), CBLASTParams::IsNucInput(), CBLASTSearchOptionsPanel::LoadSettings(), CBLASTToolManager::m_Descriptor, CBLASTToolManager::m_NucObjects, CBLASTToolManager::m_OptionsPanel, CBLASTToolManager::m_Params, CBLASTToolManager::m_ParentWindow, CBLASTToolManager::m_ProtObjects, CBLASTToolManager::m_RegPath, NULL, CBLASTSearchOptionsPanel::SetParams(), CAlgoToolManagerParamsPanel::SetRegistryPath(), CBLASTSearchOptionsPanel::Setup(), CBLASTToolManager::x_IsNucInput(), and CBLASTToolManager::x_SelectCompatibleInputObjects().

Referenced by CBLASTToolManager::DoTransition().

◆ x_CreateParamsPanelIfNeeded() [1/18] bool CBLASTToolManager::x_CreateParamsPanelIfNeeded ( ) protectedvirtual ◆ x_CreateParamsPanelIfNeeded() [2/18] bool CCleanupAlignmentsToolManager::x_CreateParamsPanelIfNeeded ( ) protectedvirtual

returns / creates Parameters panel, override in derived classes see cpp file for example

Implements CAlgoToolManagerBase.

Definition at line 99 of file cleanup_alignments_tool_manager.cpp.

References CCleanupAlignmentsParamsPanel::Create(), CCleanupAlignmentsParamsPanel::LoadSettings(), CCleanupAlignmentsToolManager::m_Alignments, SCleanupAlignmentsParams::m_AlnMgr_PreserveRows, CCleanupAlignmentsToolManager::m_Params, CCleanupAlignmentsToolManager::m_ParamsPanel, CAlgoToolManagerBase::m_ParentWindow, CAlgoToolManagerBase::m_RegPath, NULL, CCleanupAlignmentsParamsPanel::SetParams(), CCleanupAlignmentsParamsPanel::SetRegistryPath(), CCleanupAlignmentsToolManager::x_AreSelfAlignmentsOnly(), and CCleanupAlignmentsToolManager::x_SelectCompatibleInputObjects().

◆ x_CreateParamsPanelIfNeeded() [3/18] bool CClustalOmegaTool::x_CreateParamsPanelIfNeeded ( ) protectedvirtual

returns / creates Parameters panel, override in derived classes see cpp file for example

Implements CAlgoToolManagerBase.

Definition at line 82 of file clustal_omega_tool.cpp.

References CClustalOmegaToolPanel::LoadSettings(), CClustalOmegaTool::m_Objects, CClustalOmegaTool::m_Panel, CClustalOmegaTool::m_Params, CAlgoToolManagerBase::m_ParentWindow, CAlgoToolManagerBase::m_RegPath, NULL, CClustalOmegaToolPanel::SetData(), CClustalOmegaToolPanel::SetObjects(), CClustalOmegaToolPanel::SetRegistryPath(), SYMBOL_CCLUSTALOMEGATOOLPANEL_STYLE, wxID_ANY, and CClustalOmegaTool::x_SelectCompatibleInputObjects().

◆ x_CreateParamsPanelIfNeeded() [4/18] bool CClustalwTool::x_CreateParamsPanelIfNeeded ( ) protectedvirtual

returns / creates Parameters panel, override in derived classes see cpp file for example

Implements CAlgoToolManagerBase.

Definition at line 82 of file clustalw_tool.cpp.

References CClustalwToolPanel::LoadSettings(), CClustalwTool::m_Objects, CClustalwTool::m_Panel, CClustalwTool::m_Params, CAlgoToolManagerBase::m_ParentWindow, CAlgoToolManagerBase::m_RegPath, NULL, CClustalwToolPanel::SetData(), CClustalwToolPanel::SetObjects(), CClustalwToolPanel::SetRegistryPath(), SYMBOL_CCLUSTALWTOOLPANEL_STYLE, wxID_ANY, and CClustalwTool::x_SelectCompatibleInputObjects().

◆ x_CreateParamsPanelIfNeeded() [5/18] bool CCreateGeneModelToolManager::x_CreateParamsPanelIfNeeded ( ) protectedvirtual

returns / creates Parameters panel, override in derived classes see cpp file for example

Implements CAlgoToolManagerBase.

Definition at line 103 of file create_gene_model_tool_manager.cpp.

References CCreateGeneModelParamsPanel::Create(), CCreateGeneModelParamsPanel::LoadSettings(), CCreateGeneModelToolManager::m_Alignments, CCreateGeneModelToolManager::m_Params, CCreateGeneModelToolManager::m_ParamsPanel, CAlgoToolManagerBase::m_ParentWindow, CAlgoToolManagerBase::m_RegPath, NULL, CCreateGeneModelParamsPanel::SetParams(), CCreateGeneModelParamsPanel::SetRegistryPath(), and CCreateGeneModelToolManager::x_SelectCompatibleInputObjects().

◆ x_CreateParamsPanelIfNeeded() [6/18] bool CFindOverlapTool::x_CreateParamsPanelIfNeeded ( ) protectedvirtual

returns / creates Parameters panel, override in derived classes see cpp file for example

Implements CAlgoToolManagerBase.

Definition at line 108 of file find_overlap_tool.cpp.

References CFindOverlapPanel::LoadSettings(), CFindOverlapTool::m_Panel, CFindOverlapTool::m_Params, CAlgoToolManagerBase::m_ParentWindow, CAlgoToolManagerBase::m_RegPath, CFindOverlapTool::m_SeqIds, NULL, CFindOverlapPanel::SetData(), CFindOverlapPanel::SetObjects(), CAlgoToolManagerParamsPanel::SetRegistryPath(), SYMBOL_CFINDOVERLAPPANEL_STYLE, wxID_ANY, and CFindOverlapTool::x_SelectCompatibleInputObjects().

◆ x_CreateParamsPanelIfNeeded() [7/18] bool CGroupAlignmentsToolManager::x_CreateParamsPanelIfNeeded ( ) protectedvirtual

returns / creates Parameters panel, override in derived classes see cpp file for example

Implements CAlgoToolManagerBase.

Definition at line 91 of file group_alignments_tool_manager.cpp.

References CGroupAlignmentsParamsPanel::Create(), CGroupAlignmentsParamsPanel::LoadSettings(), CGroupAlignmentsToolManager::m_Alignments, CGroupAlignmentsToolManager::m_Params, CGroupAlignmentsToolManager::m_ParamsPanel, CAlgoToolManagerBase::m_ParentWindow, CAlgoToolManagerBase::m_RegPath, NULL, CGroupAlignmentsParamsPanel::SetParams(), CGroupAlignmentsParamsPanel::SetRegistryPath(), and CGroupAlignmentsToolManager::x_SelectCompatibleInputObjects().

◆ x_CreateParamsPanelIfNeeded() [8/18] bool CKalignTool::x_CreateParamsPanelIfNeeded ( ) protectedvirtual

returns / creates Parameters panel, override in derived classes see cpp file for example

Implements CAlgoToolManagerBase.

Definition at line 81 of file kalign_tool.cpp.

References CKalignToolPanel::LoadSettings(), CKalignTool::m_Objects, CKalignTool::m_Panel, CKalignTool::m_Params, CAlgoToolManagerBase::m_ParentWindow, CAlgoToolManagerBase::m_RegPath, NULL, CKalignToolPanel::SetData(), CKalignToolPanel::SetObjects(), CKalignToolPanel::SetRegistryPath(), SYMBOL_CKALIGNTOOLPANEL_STYLE, wxID_ANY, and CKalignTool::x_SelectCompatibleInputObjects().

◆ x_CreateParamsPanelIfNeeded() [9/18] bool CMafftTool::x_CreateParamsPanelIfNeeded ( ) protectedvirtual

returns / creates Parameters panel, override in derived classes see cpp file for example

Implements CAlgoToolManagerBase.

Definition at line 81 of file mafft_tool.cpp.

References CMafftToolPanel::LoadSettings(), CMafftTool::m_Objects, CMafftTool::m_Panel, CMafftTool::m_Params, CAlgoToolManagerBase::m_ParentWindow, CAlgoToolManagerBase::m_RegPath, NULL, CMafftToolPanel::SetData(), CMafftToolPanel::SetObjects(), CMafftToolPanel::SetRegistryPath(), SYMBOL_CMAFFTTOOLPANEL_STYLE, wxID_ANY, and CMafftTool::x_SelectCompatibleInputObjects().

◆ x_CreateParamsPanelIfNeeded() [10/18] bool CMergeAlignmentsToolManager::x_CreateParamsPanelIfNeeded ( ) protectedvirtual

returns / creates Parameters panel, override in derived classes see cpp file for example

Implements CAlgoToolManagerBase.

Definition at line 103 of file merge_alignments_tool_manager.cpp.

References CMergeAlignmentsParamsPanel::Create(), CMergeAlignmentsParamsPanel::LoadSettings(), CMergeAlignmentsToolManager::m_Alignments, CMergeAlignmentsToolManager::m_Params, CMergeAlignmentsToolManager::m_ParamsPanel, CAlgoToolManagerBase::m_ParentWindow, CAlgoToolManagerBase::m_RegPath, NULL, CMergeAlignmentsParamsPanel::SetParams(), CMergeAlignmentsParamsPanel::SetRegistryPath(), and CMergeAlignmentsToolManager::x_SelectCompatibleInputObjects().

◆ x_CreateParamsPanelIfNeeded() [11/18] bool CMuscleTool::x_CreateParamsPanelIfNeeded ( ) protectedvirtual

returns / creates Parameters panel, override in derived classes see cpp file for example

Implements CAlgoToolManagerBase.

Definition at line 81 of file muscle_tool.cpp.

References CMuscleToolPanel::LoadSettings(), CMuscleTool::m_Objects, CMuscleTool::m_Panel, CMuscleTool::m_Params, CAlgoToolManagerBase::m_ParentWindow, CAlgoToolManagerBase::m_RegPath, NULL, CMuscleToolPanel::SetData(), CMuscleToolPanel::SetObjects(), CMuscleToolPanel::SetRegistryPath(), SYMBOL_CMUSCLETOOLPANEL_STYLE, wxID_ANY, and CMuscleTool::x_SelectCompatibleInputObjects().

◆ x_CreateParamsPanelIfNeeded() [12/18] bool CNGAlignTool::x_CreateParamsPanelIfNeeded ( ) protectedvirtual ◆ x_CreateParamsPanelIfNeeded() [13/18] bool CProSplignTool::x_CreateParamsPanelIfNeeded ( ) protectedvirtual

returns / creates Parameters panel, override in derived classes see cpp file for example

Implements CAlgoToolManagerBase.

Definition at line 148 of file prosplign_tool.cpp.

References CProSplignPanel::LoadSettings(), CProSplignTool::m_NAObjects, CProSplignTool::m_Panel, CProSplignTool::m_Params, CAlgoToolManagerBase::m_ParentWindow, CProSplignTool::m_ProteinObjects, CAlgoToolManagerBase::m_RegPath, NULL, CProSplignPanel::SetData(), CProSplignPanel::SetObjects(), CProSplignPanel::SetRegistryPath(), SYMBOL_CPROSPLIGNPANEL_STYLE, wxID_ANY, and CProSplignTool::x_SelectCompatibleInputObjects().

◆ x_CreateParamsPanelIfNeeded() [14/18] bool CSplignTool::x_CreateParamsPanelIfNeeded ( ) protectedvirtual

returns / creates Parameters panel, override in derived classes see cpp file for example

Implements CAlgoToolManagerBase.

Definition at line 97 of file splign_tool.cpp.

References map_checker< Container >::empty(), CSplignPanel::LoadSettings(), CSplignTool::m_GenomicObjects, CSplignTool::m_NAObjects, CSplignTool::m_Panel, CSplignTool::m_Params, CAlgoToolManagerBase::m_ParentWindow, CAlgoToolManagerBase::m_RegPath, NULL, CSplignPanel::SetData(), CSplignPanel::SetObjects(), CSplignPanel::SetRegistryPath(), SYMBOL_CSPLIGNPANEL_STYLE, wxID_ANY, and CSplignTool::x_SelectCompatibleInputObjects().

◆ x_CreateParamsPanelIfNeeded() [15/18] bool CCommonTaxTreeTool::x_CreateParamsPanelIfNeeded ( ) protectedvirtual

returns / creates Parameters panel, override in derived classes see cpp file for example

Implements CAlgoToolManagerBase.

Definition at line 82 of file taxtree_tool.cpp.

References CTaxTreeToolPanel::LoadSettings(), CCommonTaxTreeTool::m_Objects, CCommonTaxTreeTool::m_Panel, CCommonTaxTreeTool::m_Params, CAlgoToolManagerBase::m_ParentWindow, CAlgoToolManagerBase::m_RegPath, NULL, CTaxTreeToolPanel::SetData(), CTaxTreeToolPanel::SetObjects(), CTaxTreeToolPanel::SetRegistryPath(), SYMBOL_CTAXTREETOOLPANEL_STYLE, wxID_ANY, and CCommonTaxTreeTool::x_SelectCompatibleInputObjects().

◆ x_CreateParamsPanelIfNeeded() [16/18] bool CTreeBuilderTool::x_CreateParamsPanelIfNeeded ( ) protectedvirtual

returns / creates Parameters panel, override in derived classes see cpp file for example

Implements CAlgoToolManagerBase.

Definition at line 122 of file tree_builder_tool.cpp.

References CTreeBuilderPanel::Create(), CTreeBuilderPanel::LoadSettings(), CTreeBuilderTool::m_Panel, CTreeBuilderTool::m_Params, CAlgoToolManagerBase::m_ParentWindow, CAlgoToolManagerBase::m_RegPath, CTreeBuilderTool::m_SeqIds, NULL, CTreeBuilderPanel::SetData(), CTreeBuilderPanel::SetObjects(), CAlgoToolManagerParamsPanel::SetRegistryPath(), and CTreeBuilderTool::x_SelectCompatibleInputObjects().

◆ x_CreateParamsPanelIfNeeded() [17/18] bool CAdvancedCleanupTool::x_CreateParamsPanelIfNeeded ( ) protectedvirtual

returns / creates Parameters panel, override in derived classes see cpp file for example

Implements CAlgoToolManagerBase.

Definition at line 77 of file advanced_cleanup_tool.cpp.

References CAdvancedCleanupParamsPanel::LoadSettings(), CAdvancedCleanupTool::m_Alignments, CAdvancedCleanupTool::m_Panel, CAdvancedCleanupTool::m_Params, CAlgoToolManagerBase::m_ParentWindow, CAlgoToolManagerBase::m_RegPath, NULL, CAdvancedCleanupParamsPanel::SetData(), CAdvancedCleanupParamsPanel::SetObjects(), CAdvancedCleanupParamsPanel::SetRegistryPath(), SYMBOL_CADVANCEDCLEANUPPARAMSPANEL_STYLE, wxID_ANY, and CAdvancedCleanupTool::x_SelectCompatibleInputObjects().

◆ x_CreateParamsPanelIfNeeded() [18/18] bool CCreateNeedlemanWunschToolManager::x_CreateParamsPanelIfNeeded ( ) protectedvirtual

returns / creates Parameters panel, override in derived classes see cpp file for example

Implements CAlgoToolManagerBase.

Definition at line 109 of file create_needleman_wunsch_tool_manager.cpp.

References CAlignNeedlemanWunschPanel::Create(), CAlignNeedlemanWunschPanel::LoadSettings(), CCreateNeedlemanWunschToolManager::m_Objects, CCreateNeedlemanWunschToolManager::m_Panel, CCreateNeedlemanWunschToolManager::m_Params, CAlgoToolManagerBase::m_ParentWindow, CAlgoToolManagerBase::m_RegPath, NULL, CAlignNeedlemanWunschPanel::SetData(), CAlignNeedlemanWunschPanel::SetObjects(), CAlignNeedlemanWunschPanel::SetRegistryPath(), and CCreateNeedlemanWunschToolManager::x_SelectCompatibleInputObjects().

◆ x_CreateProjectItems() [1/12] void CNetBlastLoadingJob::x_CreateProjectItems ( ) protectedvirtual

iterates on the given RIDs and creates Project Items or accumulates error

Implements CDataLoadingAppJob.

Definition at line 524 of file blast_jobs.cpp.

References CNetBlastJobDescriptor::Check(), CNetBlastJobDescriptor::eCompleted, CNetBlastJobDescriptor::eExpired, CNetBlastJobDescriptor::eFailed, CNetBlastJobDescriptor::eInitial, CNetBlastJobDescriptor::eRetrieved, CNetBlastJobDescriptor::eSubmitted, CNetBlastJobDescriptor::GetErrors(), CNetBlastJobDescriptor::GetRemoteBlast(), CNetBlastJobDescriptor::GetRID(), CNetBlastJobDescriptor::GetState(), i, CNetBlastLoadingJob::m_Descriptors, CNetBlastLoadingJob::m_Errors, CAppJob::m_Mutex, results, CNetBlastJobDescriptor::Retrieve(), and CNetBlastLoadingJob::x_CreateProjectItemsFromBlastResult().

◆ x_CreateProjectItems() [2/12] void CBLASTSeqToolJob::x_CreateProjectItems ( ) protectedvirtual

override this function in derived classes and populate m_Items.

If data loaders are needed, they should be created here too.

Implements CDataLoadingAppJob.

Definition at line 141 of file blast_seq_tool_job.cpp.

References CMappingRanges::AddConversion(), CDataLoadingAppJob::AddProjectItem(), CLBLASTObjectLoader::CreateLoader(), CDebugDumpable::DebugDumpText(), CSeq_id_Base::e_Local, CTime::eCurrent, CLabel::eDefault, CBLASTParams::eLocalDB, eNa_strand_plus, CExec::eNoWait, EProgramToTaskName(), ERR_POST, Error(), CSeq_loc_Mapper_Base::eSeq_nuc, CSeq_loc_Mapper_Base::eSeq_prot, CBLASTParams::eSequences, eSerial_AsnText, FindCompartments(), CSeq_annot_Base::C_Data::GetAlign(), CScope::GetBioseqHandle(), CBLASTParams::GetCurrParams(), CBLASTParams::GetCurrProgram(), CSeq_annot_Base::GetData(), CIOException::GetErrCodeString(), CProcess::CExitInfo::GetExitCode(), CSeq_id_Handle::GetHandle(), CSeq_loc::GetId(), CLabel::GetLabel(), GetLength(), CBLASTParams::GetLocalDBLoader(), CBLASTParams::GetLocalNucDB(), CBLASTParams::GetLocalProtDB(), CException::GetMsg(), CBlastOptionsHandle::GetOptions(), CRef< C, Locker >::GetPointer(), CExec::CResult::GetProcessHandle(), CBLASTParams::GetSeqLocs(), GetStart(), CSysPath::GetStdPath(), GetStrand(), CBLASTParams::GetSubjectType(), CBLASTParams::GetSubjSeqLocs(), CDirEntry::GetTmpName(), CBLASTParams::GetWmDir(), i, Info(), NStr::IntToString(), CSeq_annot::IsAlign(), CJobCancelable::IsCanceled(), CBLASTParams::IsCompartmentsRequested(), CBLASTParams::IsNucInput(), CBioseq_Handle::IsNucleotide(), CRef< C, Locker >::IsNull(), CBLASTParams::IsStandaloneRequested(), CBLASTParams::IsSubjNucInput(), CSeq_loc_Base::IsWhole(), ITERATE, kArgDb, kArgOutput, kArgQuery, kArgSubject, kInfiniteTimeoutMs, kInvalidProcHandle, label, LOG_POST, CBLASTParams::SProgParams::m_MaskLowercase, CBLASTParams::SProgParams::m_MaskRepeats, CBLASTSeqToolJob::m_Params, CBLASTSeqToolJob::m_ProcHandle, CBLASTParams::SProgParams::m_WM_TaxId, CSeq_loc_Mapper_Base::Map(), MSerial_AsnText, NON_CONST_ITERATE, nuc, NULL, CObjectOStream::Open(), CDirEntry::Remove(), CBl2Seq::Run(), CBLASTSeqToolJob::s_BlastInterrupt(), SSeqLoc::scope, SSeqLoc::seqloc, CSeq_align_set_Base::Set(), CSeq_annot::SetCreateDate(), CSeq_annot_Base::SetData(), CBl2Seq::SetInterruptCallback(), CProjectItem_Base::SetItem(), CProjectItem_Base::SetLabel(), CSeq_annot::SetNameDesc(), CSeq_loc_Mapper_Base::SetSeqTypeById(), CSeq_annot::SetTitleDesc(), si, CExec::SpawnV(), CBLASTParams::ToArgVecBlastOptions(), ToWxString(), CProcess::Wait(), Warning(), WindowMaskerPathGet(), WindowMaskerPathInit(), CFastaOstream::Write(), wxT, CAppJob::x_SetStatusText(), and x_ToBlastVec().

◆ x_CreateProjectItems() [3/12] void CCleanupAlignmentsJob::x_CreateProjectItems ( ) protectedvirtual

override this function in derived classes and populate m_Items.

If data loaders are needed, they should be created here too.

Implements CDataLoadingAppJob.

Definition at line 230 of file cleanup_alignments_tool_manager.cpp.

References CDataLoadingAppJob::AddProjectItem(), CScoreBuilder::AddScore(), cleanup(), copy(), SCleanupAlignmentsParams::eAlignmentManager, CAlignCleanup::eAnchoredAlign, CTime::eCurrent, CLabel::eDefault, SCleanupAlignmentsParams::eHitFilter, eNa_strand_minus, eNa_strand_plus, CSeq_align::eScore_PercentIdentity, CSeq_align_Base::eType_disc, CDense_seg::FromTranscript(), CSeq_align_set_Base::Get(), CSeq_align_Base::C_Segs::GetDisc(), CAlignShadow::GetId(), CLabel::GetLabel(), CAlignShadow::GetQueryStart(), CAlignShadow::GetQueryStrand(), CBlastTabular::GetScore(), CSeq_align_Base::GetSegs(), CAlignShadow::GetSubjStart(), CAlignShadow::GetSubjStrand(), CAlignShadow::GetTranscript(), CAlignGroup::GroupByStrand(), CSeq_align_Base::C_Segs::IsDisc(), ITERATE, SCleanupAlignmentsParams::m_Algo, SCleanupAlignmentsParams::m_Alignments, SCleanupAlignmentsParams::m_AlnMgr_FillUnaligned, SCleanupAlignmentsParams::m_AlnMgr_PreserveRows, SCleanupAlignmentsParams::m_AlnMgr_Sort, SCleanupAlignmentsParams::m_HitFilter_MinIdentity, SCleanupAlignmentsParams::m_HitFilter_MinLength, CCleanupAlignmentsJob::m_Params, NCBI_USER_THROW, NON_CONST_ITERATE, remove_if(), CRef< C, Locker >::Reset(), CDense_seg_Base::ResetStrands(), CHitFilter< THit >::s_RunGreedy(), CAlignShadow::s_RunLengthDecode(), CDense_seg_Base::SetIds(), CProjectItem_Base::SetItem(), CProjectItem_Base::SetLabel(), CDense_seg_Base::SetScores(), CSeq_align_Base::SetSegs(), and CSeq_align_Base::SetType().

◆ x_CreateProjectItems() [4/12] void CGroupAlignmentsJob::x_CreateProjectItems ( ) protectedvirtual

override this function in derived classes and populate m_Items.

If data loaders are needed, they should be created here too.

Implements CDataLoadingAppJob.

Definition at line 198 of file group_alignments_tool_manager.cpp.

References CDataLoadingAppJob::AddProjectItem(), CTime::eCurrent, CLabel::eDefault, eUnknown, CAlignGroup::fEST, CAlignGroup::fGB_EMBL_DDBJ, CAlignGroup::fHTGS, flags, CAlignGroup::fPatent, CAlignGroup::fRefSeq, CAlignGroup::fRefSeqPredicted, CAlignGroup::fWGS, CSeq_annot_Base::C_Data::GetAlign(), CSeq_annot_Base::GetData(), CLabel::GetLabel(), CSeq_annot_Base::GetName(), CAlignGroup::GroupByLikeTaxIds(), CAlignGroup::GroupBySeqIds(), CAlignGroup::GroupBySequenceType(), CAlignGroup::GroupByStrand(), CAlignGroup::GroupByTaxIds(), ITERATE, SGroupAlignmentsParams::m_Alignments, SGroupAlignmentsParams::m_GroupByEST, SGroupAlignmentsParams::m_GroupByGenBank, SGroupAlignmentsParams::m_GroupByHTGS, SGroupAlignmentsParams::m_GroupByLikeTaxId, SGroupAlignmentsParams::m_GroupByPatent, SGroupAlignmentsParams::m_GroupByPredictedRefSeq, SGroupAlignmentsParams::m_GroupByRefSeq, SGroupAlignmentsParams::m_GroupBySeqId, SGroupAlignmentsParams::m_GroupByStrand, SGroupAlignmentsParams::m_GroupByTaxId, SGroupAlignmentsParams::m_GroupByWGS, CGroupAlignmentsJob::m_Params, NCBI_THROW, NON_CONST_ITERATE, CRef< C, Locker >::Reset(), CSeq_annot_Base::ResetName(), s_GetAnnotName(), CSeq_annot::SetCreateDate(), CSeq_annot_Base::SetData(), CProjectItem_Base::SetItem(), CProjectItem_Base::SetLabel(), CSeq_annot::SetNameDesc(), and tag.

◆ x_CreateProjectItems() [5/12] void CMergeAlignmentsJob::x_CreateProjectItems ( ) protectedvirtual

override this function in derived classes and populate m_Items.

If data loaders are needed, they should be created here too.

Implements CDataLoadingAppJob.

Definition at line 186 of file merge_alignments_tool_manager.cpp.

References CDataLoadingAppJob::AddProjectItem(), BuildAln(), count, CreateAnchoredAlnVec(), CreateSeqAlignFromEachPairwiseAln(), CSeq_align_Base::C_Segs::e_Denseg, CAlnUserOptions::eBothDirections, CTime::eCurrent, CLabel::eDefault, CAlnUserOptions::eMergeAllSeqs, CAlnUserOptions::eQuerySeqMergeOnly, CAlnUserOptions::eReverse, Error(), CSeq_align_Base::eType_partial, eUnknown, CDense_seg::FillUnaligned(), flags, CAnchoredAln::GetAnchorRow(), CSeq_id_Handle::GetHandle(), CAlnStats< _TAlnIdVec >::GetIdVec(), CLabel::GetLabel(), CException::GetMsg(), CAnchoredAln::GetPairwiseAlns(), CAlignGroup::GroupByStrand(), i, CAlnContainer::insert(), set< Key, Compare >::insert(), NStr::IntToString(), ITERATE, LOG_POST, SMergeAlignmentsParams::m_Alignments, SMergeAlignmentsParams::m_Direction, CAlnUserOptions::m_Direction, SMergeAlignmentsParams::m_FillUnaligned, SMergeAlignmentsParams::m_MergeAlgo, CAlnUserOptions::m_MergeAlgo, SMergeAlignmentsParams::m_MergeFlags, CMergeAlignmentsJob::m_Params, msg(), NCBI_THROW, NON_CONST_ITERATE, CAlnIdMap< _TAlnVec, TAlnSeqIdExtract >::push_back(), CRef< C, Locker >::Reset(), CProjectItem_Base::SetItem(), CProjectItem_Base::SetLabel(), CAlnUserOptions::SetMergeFlags(), CAlnContainer::size(), CSeq_align::Validate(), and Warning().

◆ x_CreateProjectItems() [6/12] void CMSAToolJob::x_CreateProjectItems ( ) protectedvirtual

override this function in derived classes and populate m_Items.

If data loaders are needed, they should be created here too.

Implements CDataLoadingAppJob.

Definition at line 215 of file msa_tool_job.cpp.

References CDataLoadingAppJob::AddProjectItem(), CTime::eCurrent, CLabel::eDefault, Error(), CSeq_loc_Mapper_Base::eSeq_nuc, CSeq_loc_Mapper_Base::eSeq_prot, eUnknown, CFastaReader::fParseGaps, CLabel::GetLabel(), CException::GetMsg(), CRef< C, Locker >::GetPointer(), CJobCancelable::IsCanceled(), ITERATE, LOG_POST, CMSAToolJob::m_CmdLine, CMSAToolJob::m_PId, CMSAToolJob::m_Ranges, CDataLoadingAppJob::m_Scope, CMSAToolJob::m_SeqTypes, CMSAToolJob::m_TmpOut, CMSAToolJob::m_TmpTreeOut, CMSAToolJob::m_ToolName, CSeq_loc_Mapper_Base::Map(), NCBI_THROW, proc, CFastaReader::ReadAlignedSet(), CRef< C, Locker >::Reset(), CAnnotdesc_Base::SetComment(), CSeq_annot::SetCreateDate(), CSeq_annot_Base::SetData(), CProjectItem_Base::SetDescr(), CProjectItem_Base::SetItem(), CProjectItem_Base::SetLabel(), CSeq_annot::SetNameDesc(), CSeq_loc_Mapper_Base::SetSeqTypeById(), ncbi::grid::netcache::search::fields::size, string, CException::what(), and CMSAToolJob::x_AddTreeProjectItem().

◆ x_CreateProjectItems() [7/12] void CNGAlignJob::x_CreateProjectItems ( ) protectedvirtual

override this function in derived classes and populate m_Items.

If data loaders are needed, they should be created here too.

Implements CDataLoadingAppJob.

Definition at line 301 of file ngalign_job.cpp.

References CDataLoadingAppJob::AddProjectItem(), CurrentTime(), CSeq_loc_Base::e_Whole, CLabel::eDefault, Error(), CNGAlignParams::GetFilterMode(), CLabel::GetLabel(), CConstRef< C, Locker >::GetPointer(), CNGAlignParams::GetSubject(), CSeq_align_set_Base::IsSet(), ITERATE, LOG_POST, CNGAlignParams::LogDump(), CNGAlignJob::m_Params, NON_CONST_ITERATE, NULL, SConstScopedObject::object, s_CallAligner(), SConstScopedObject::scope, CSeq_align_set_Base::Set(), CSeq_annot::SetCreateDate(), CSeq_annot_Base::SetData(), CSeq_loc::SetId(), CProjectItem_Base::SetItem(), CProjectItem_Base::SetLabel(), CSeq_annot::SetNameDesc(), CNGAlignParams::SetQueries(), CNgAligner::SetQuery(), CNgAligner::SetSubject(), CSeq_annot::SetTitleDesc(), and subject.

◆ x_CreateProjectItems() [8/12] void CPhyloTreeJob::x_CreateProjectItems ( ) protectedvirtual ◆ x_CreateProjectItems() [9/12] void CTaxTreeToolJob::x_CreateProjectItems ( ) protectedvirtual

override this function in derived classes and populate m_Items.

If data loaders are needed, they should be created here too.

Implements CDataLoadingAppJob.

Definition at line 77 of file taxtree_tool_job.cpp.

References CDataLoadingAppJob::AddProjectItem(), bm::BM_GAP, CLabel::eDefault, eGetId_Canonical, map_checker< Container >::end(), ERR_POST, eTaxTree_Label, eTaxTree_SeqId, eTaxTree_TaxId, eUnknown, map_checker< Container >::find(), CScope::GetBioseqHandle(), CScope::GetGi(), CSeq_id_Base::GetGi(), GetId(), CSeq_loc::GetId(), CLabel::GetLabel(), CTaxon1::GetLastError(), CBioseq_Handle::GetNonLocalIdOrNull(), CTaxon1::GetPopsetJoin(), CBioseq_Handle::GetSeqId(), GetTaxId(), CTaxon1::GetTaxId4GI(), CScope::GetTaxIds(), CTaxon1::GetTreeIterator(), CTaxon1::Init(), NStr::IntToString(), CTaxon1::IsAlive(), CSeq_id_Base::IsGi(), ITERATE, label, CTaxon1::LoadNode(), LOG_POST, CTaxTreeToolJob::m_Params, NCBI_THROW, CProjectItem_Base::SetItem(), CProjectItem_Base::SetLabel(), CBioTreeContainer_Base::SetNodes(), CTaxTreeToolParams::SetObjects(), CBioTreeContainer_Base::SetTreetype(), NStr::SizetToString(), and ZERO_GI.

◆ x_CreateProjectItems() [10/12] void CDebugMacroToolJob::x_CreateProjectItems ( ) protectedvirtual ◆ x_CreateProjectItems() [11/12] void CCreateNeedlemanWunschJob::x_CreateProjectItems ( ) protectedvirtual

override this function in derived classes and populate m_Items.

If data loaders are needed, they should be created here too.

Implements CDataLoadingAppJob.

Definition at line 200 of file create_needleman_wunsch_tool_manager.cpp.

References CSeq_annot::AddComment(), CDataLoadingAppJob::AddProjectItem(), CNWFormatter::AsSeqAlign(), CSeq_loc::Assign(), CTime::AsString(), CSeq_loc_Base::e_Whole, CNeedlemanWunschToolParams::eBoth, CBioseq_Handle::eCoding_Iupac, CTime::eCurrent, CLabel::eDefault, CNeedlemanWunschToolParams::eLeft, eNa_strand_plus, CNeedlemanWunschToolParams::eRight, eUnknown, CNeedlemanWunschToolParams::GetBandSize(), CScope::GetBioseqHandle(), CNeedlemanWunschToolParams::GetFirstSeqFreeEnds(), CNeedlemanWunschToolParams::GetGapExtendCost(), CNeedlemanWunschToolParams::GetGapOpenCost(), GetId(), CLabel::GetLabel(), COpenRange< Position >::GetLength(), CNeedlemanWunschToolParams::GetMatchCost(), CNeedlemanWunschToolParams::GetMismatchCost(), CNeedlemanWunschToolParams::GetSecondSeqFreeEnds(), CSeqVector::GetSeqData(), CBioseq_Handle::GetSeqId(), CSeq_loc::GetTotalRange(), Info(), CJobCancelable::IsCanceled(), CSeqVector::IsNucleotide(), IsOneBioseq(), CSeq_loc_Base::IsWhole(), ITERATE, LOG_POST, CCreateNeedlemanWunschJob::m_Params, CSeq_loc_Mapper_Base::Map(), NCBI_THROW, NCBISM_Blosum62, NON_CONST_ITERATE, NULL, output, CRef< C, Locker >::Reset(), s_ProgressCallback(), CAnnotdesc_Base::SetCreate_date(), CSeq_annot::SetCreateDate(), CSeq_annot_Base::SetData(), CSeq_annot_Base::SetDesc(), CSeq_loc::SetId(), CSeq_loc::SetInt(), CProjectItem_Base::SetItem(), CProjectItem_Base::SetLabel(), CSeq_annot::SetNameDesc(), CNeedlemanWunschToolParams::SetObjects(), CSeq_align_Base::SetSegs(), CDate_Base::SetStr(), CSeqVector::size(), str(), NStr::ToUpper(), and CSeq_loc_Base::Which().

◆ x_CreateProjectItems() [12/12] void CBLASTSeqToolJob::x_CreateProjectItems ( vector< CRef< objects::CSeq_align_set > > &  aligns ) protected ◆ x_CreateProjectItemsFromBlastResult() void CNetBlastLoadingJob::x_CreateProjectItemsFromBlastResult ( objects::CSeq_align_set &  results, CRef< blast::CRemoteBlast >  RemoteBlast  ) protected ◆ x_CreateRemoteBlastIfNeeded() void CNetBlastJobDescriptor::x_CreateRemoteBlastIfNeeded ( ) protected ◆ x_CreateTreeItems() void CBLAST_DB_Dialog::x_CreateTreeItems ( ) protected ◆ x_DoSearch()

performs searching, assuming that params are correct; Implement in derived classes

Implements CSearchJobBase.

Definition at line 387 of file net_blast_dm_search_tool.cpp.

References CObjectList::AddRow(), IAppJob::eCompleted, NStr::FindNoCase(), CNetBLASTUIDataSource::GetJobDescriptors(), GetNetBlastJobDescription(), CNetBlastJobDescriptor::GetState(), i, CJobCancelable::IsCanceled(), CSearchJobBase::m_AccList, CNetBLAST_DMSearchQuery::m_FilterStr, CNetBLAST_DMSearchJob::m_NetBlastDS, CNetBLAST_DMSearchJob::m_Query, CNetBLAST_DMSearchQuery::m_States, n, NULL, and skNumColumns.

◆ x_FillQueryList() void CBLASTSearchOptionsPanel::x_FillQueryList ( ) protected

Definition at line 611 of file blast_search_options_panel.cpp.

References ctll::empty(), i, CBLASTParams::IsNucInput(), CBLASTSearchOptionsPanel::m_CurrentQuerySet, CBLASTSearchOptionsPanel::m_NucObjects, CBLASTSearchOptionsPanel::m_Params, CBLASTSearchOptionsPanel::m_ProtObjects, CBLASTSearchOptionsPanel::m_QueryListCtrl, CBLASTSearchOptionsPanel::m_SubjectListCtrl, s_UseSets(), CwxTableListCtrl::SelectAll(), and CObjectListWidget::SetObjects().

Referenced by CBLASTSearchOptionsPanel::OnQuerySequenceSetSelected(), and CBLASTSearchOptionsPanel::x_OnInputTypeChanged().

◆ x_FillSubjectList() void CBLASTSearchOptionsPanel::x_FillSubjectList ( ) protected

Definition at line 719 of file blast_search_options_panel.cpp.

References ctll::empty(), i, CBLASTParams::IsSubjNucInput(), CBLASTSearchOptionsPanel::m_CurrentSubjectSet, CBLASTSearchOptionsPanel::m_NucObjects, CBLASTSearchOptionsPanel::m_Params, CBLASTSearchOptionsPanel::m_ProtObjects, CBLASTSearchOptionsPanel::m_SubjectListCtrl, s_UseSets(), CwxTableListCtrl::SelectAll(), and CObjectListWidget::SetObjects().

Referenced by CBLASTSearchOptionsPanel::OnSubjectSequenceSetSelected(), and CBLASTSearchOptionsPanel::x_UpdateSubjects().

◆ x_FilterItems() void CBLAST_DB_Dialog::x_FilterItems ( const string &  query ) protected

Definition at line 431 of file blast_db_dialog.cpp.

References NStr::FindNoCase(), CBLAST_Dlg_Item::GetLabel(), CBLAST_Dlg_Item::GetParent(), CBLAST_Dlg_Item::IsVisible(), label, CBLAST_DB_Dialog::m_CatItems, CBLAST_DB_Dialog::m_DbItems, CBLAST_DB_Dialog::m_Root, CBLAST_DB_Dialog::m_TreeCtrl, NON_CONST_ITERATE, query, CBLAST_Dlg_Item::SetVisible(), ToStdString(), CBLAST_DB_Dialog::x_CreateTreeItems(), and CBLAST_DB_Dialog::x_UpdateFilterStatusText().

Referenced by CBLAST_DB_Dialog::OnInitDialog(), CBLAST_DB_Dialog::OnResetBtnClick(), and CBLAST_DB_Dialog::OnSearchTextUpdated().

◆ x_FromUserObject()

reads SProgParams fields from CUser_object

Definition at line 651 of file blast_search_params.cpp.

References CUser_field_Base::C_Data::GetBool(), CUser_field_Base::GetData(), CUser_object::GetField(), CUser_field_Base::C_Data::GetInt(), CUser_field_Base::C_Data::GetReal(), CUser_object::HasField(), kDbGeneticCodeTag, keValueTag, kFilterLowComplexTag, kGeneticCodeTag, kMaskLowercaseTag, kMaskRepeatsTag, kThresholdTag, kWordSizeTag, CBLASTParams::SProgParams::m_DbGeneticCode, CBLASTParams::SProgParams::m_eValue, CBLASTParams::SProgParams::m_FilterLowComplex, CBLASTParams::SProgParams::m_MaskLowercase, CBLASTParams::SProgParams::m_MaskRepeats, CBLASTParams::SProgParams::m_QueryGeneticCode, CBLASTParams::SProgParams::m_Threshold, CBLASTParams::SProgParams::m_WordSize, CBLASTParams::NeedsDbGeneticCode(), CBLASTParams::NeedsQueryGeneticCode(), and CBLASTParams::NeedsThreshold().

Referenced by CBLASTParams::FromUserObject().

◆ x_GetCommand()

Definition at line 337 of file create_gene_model_tool_manager.cpp.

References _ASSERT, CScope::AddDefaults(), map_checker< Container >::begin(), CTSE_Handle::CanBeEdited(), CSeq_feat_Base::CanGetProduct(), CFeatureGenerator::CleanAlignment(), map_checker< Container >::clear(), cmd, CFeatureGenerator::ConvertAlignToAnnot(), CSeq_id::eContent, CTime::eCurrent, CLabel::eDefault, CCdregion_Base::eFrame_one, eGetId_Best, Error(), eUnknown, CFeatureGenerator::fCreateCdregion, CFeatureGenerator::fCreateGene, CGeneModel::fCreateGene, CFeatureGenerator::fCreateMrna, CFeatureGenerator::fForceTranscribeMrna, CFeatureGenerator::fForceTranslateCds, CFeatureGenerator::fGenerateLocalIds, CFeatureGenerator::fPropagateNcrnaFeats, NStr::fWithCommas, CScope::GetBioseqHandle(), CSeq_feat_Base::GetData(), CRange_Base::GetFrom(), GetGiForId(), CSeq_id_Handle::GetHandle(), GetId(), CSeq_loc::GetId(), GetIdHandle(), CObjectManager::GetInstance(), CLabel::GetLabel(), CSeq_id::GetLabel(), CSeq_feat_Base::GetLocation(), CException::GetMsg(), CRef< C, Locker >::GetObject(), CRef< C, Locker >::GetPointer(), CSeq_feat_Base::GetProduct(), CSeq_id_Handle::GetSeqId(), CRange_Base::GetTo(), CBioseq_Handle::GetTopLevelEntry(), CBioseq_Handle::GetTSE_Handle(), CSeq_loc_Base::GetWhole(), i, NStr::IntToString(), CSeqFeatData_Base::IsCdregion(), CSeq_id_Base::IsGi(), CCdregion_Base::IsSetCode(), CSeq_annot_Base::IsSetData(), CCdregion_Base::IsSetFrame(), CBioseq_set_Base::IsSetSeq_set(), CSeq_loc_Base::IsWhole(), ITERATE, CFeatureGenerator::kDefaultAllowedUnaligned, label, LOG_POST, SCreateGeneModelParams::m_Alignments, SCreateGeneModelParams::m_CreateCds, SCreateGeneModelParams::m_CreateGene, SCreateGeneModelParams::m_CreateMrna, CCreateGeneModelTask::m_GeneModelMap, SCreateGeneModelParams::m_GroupByGeneId, CCreateGeneModelTask::m_Items, SCreateGeneModelParams::m_MergeResults, CCreateGeneModelTask::m_Params, SCreateGeneModelParams::m_PropagateLocalIds, SCreateGeneModelParams::m_PropagateNcrnaFeats, CCreateGeneModelTask::m_Scope, SCreateGeneModelParams::m_TranscribeMrna, SCreateGeneModelParams::m_TranslateCds, msg(), NCBI_THROW, NcbiErrorBox(), NON_CONST_ITERATE, CRef< C, Locker >::Reset(), CCreateGeneModelTask::s_FindHighestFeatId(), s_RetrieveMessage(), CFeatureGenerator::SetAllowedUnaligned(), CCdregion_Base::SetCode(), CSeq_annot::SetCreateDate(), CSeq_annot_Base::SetData(), CSeq_feat_Base::SetData(), CFeatureGenerator::SetFlags(), CCdregion_Base::SetFrame(), CSeq_id_Base::SetGi(), CProjectItem_Base::SetItem(), CProjectItem_Base::SetLabel(), CSeq_feat_Base::SetLocation(), CSeq_annot::SetNameDesc(), CSeq_feat_Base::SetProduct(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), CSeq_annot::SetTitleDesc(), map_checker< Container >::size(), CCreateGeneModelTask::x_AssignIDsAndCrossLinkFeats(), CCreateGeneModelTask::x_AssignIDsAndUpdateGenes(), CCreateGeneModelTask::x_Group_By_GeneID(), CCreateGeneModelTask::x_StoreGeneratedFeats(), and ZERO_GI.

Referenced by CCreateGeneModelTask::x_Run().

◆ x_GetCommandLine() [1/6] wxString CClustalOmegaToolJob::x_GetCommandLine ( const wxString &  input, const wxString &  output, bool  is_nucleotide  ) protectedvirtual

Returns the command line, that will be used to execute the third-party tool.

Implements CMSAToolJob.

Definition at line 51 of file clustal_omega_tool_job.cpp.

References eUnknown, CClustalOmegaToolParams::GetClustalOmegaExecutable(), CClustalOmegaToolParams::GetCommandLine(), CClustalOmegaToolParams::GetGenerateTree(), input(), CClustalOmegaToolJob::m_Params, CMSAToolJob::m_TmpTreeOut, NCBI_THROW, output, and wxT.

◆ x_GetCommandLine() [2/6] wxString CClustalwToolJob::x_GetCommandLine ( const wxString &  input, const wxString &  output, bool  is_nucleotide  ) protectedvirtual

Returns the command line, that will be used to execute the third-party tool.

Implements CMSAToolJob.

Definition at line 51 of file clustalw_tool_job.cpp.

References eUnknown, CClustalwToolParams::GetClustalWExecutable(), CClustalwToolParams::GetCommandLine(), CClustalwToolParams::GetGenerateTree(), input(), CClustalwToolJob::m_Params, CMSAToolJob::m_TmpTreeOut, NCBI_THROW, output, and wxT.

◆ x_GetCommandLine() [3/6] wxString CKalignToolJob::x_GetCommandLine ( const wxString &  input, const wxString &  output, bool  is_nucleotide  ) protectedvirtual ◆ x_GetCommandLine() [4/6] wxString CMafftToolJob::x_GetCommandLine ( const wxString &  input, const wxString &  output, bool  is_nucleotide  ) protectedvirtual

Returns the command line, that will be used to execute the third-party tool.

Implements CMSAToolJob.

Definition at line 50 of file mafft_tool_job.cpp.

References eUnknown, CMafftToolParams::GetAutoFlag(), CMafftToolParams::GetCommandLine(), CMafftToolParams::GetMafftExecutable(), CMafftToolParams::GetQuietFlag(), input(), CMafftToolJob::m_Params, NCBI_THROW, output, and wxT.

◆ x_GetCommandLine() [5/6] wxString CMuscleToolJob::x_GetCommandLine ( const wxString &  input, const wxString &  output, bool  is_nucleotide  ) protectedvirtual

Returns the command line, that will be used to execute the third-party tool.

Implements CMSAToolJob.

Definition at line 57 of file muscle_tool_job.cpp.

References eUnknown, CMuscleToolParams::GetCommandLine(), CMuscleToolParams::GetGenerateTree(), CMuscleToolParams::GetMuscleExecutable(), CMuscleToolParams::GetScoringMethod(), input(), CMuscleToolJob::m_Params, CMSAToolJob::m_TmpTreeOut, NCBI_THROW, output, and wxT.

◆ x_GetCommandLine() [6/6] virtual wxString CMSAToolJob::x_GetCommandLine ( const wxString &  input, const wxString &  output, bool  is_nucleotide  ) protectedpure virtual ◆ x_GetCurrentPage() wxPanel * CNGAlignTool::x_GetCurrentPage ( ) protected ◆ x_GetCurrentSubTask() ◆ x_GetDataSource() ◆ x_GetNewOLTModel() ◆ x_GetObjects() [1/6] ◆ x_GetObjects() [2/6] ◆ x_GetObjects() [3/6] ◆ x_GetObjects() [4/6] ◆ x_GetObjects() [5/6] ◆ x_GetObjects() [6/6] ◆ x_GetOrigObject() [1/7] ◆ x_GetOrigObject() [2/7] const CObject * CAnnotCompareView::x_GetOrigObject ( ) const protectedvirtual ◆ x_GetOrigObject() [3/7] ◆ x_GetOrigObject() [4/7] ◆ x_GetOrigObject() [5/7] const CObject * CMPCrossAlignView::x_GetOrigObject ( ) const protectedvirtual ◆ x_GetOrigObject() [6/7] ◆ x_GetOrigObject() [7/7] ◆ x_GetParamsAsRegSetting() [1/17] IRegSettings * CCleanupAlignmentsToolManager::x_GetParamsAsRegSetting ( ) protectedvirtual ◆ x_GetParamsAsRegSetting() [2/17] IRegSettings * CClustalOmegaTool::x_GetParamsAsRegSetting ( ) protectedvirtual ◆ x_GetParamsAsRegSetting() [3/17] ◆ x_GetParamsAsRegSetting() [4/17] IRegSettings * CCreateGeneModelToolManager::x_GetParamsAsRegSetting ( ) protectedvirtual ◆ x_GetParamsAsRegSetting() [5/17] IRegSettings * CFindOverlapTool::x_GetParamsAsRegSetting ( ) protectedvirtual ◆ x_GetParamsAsRegSetting() [6/17] IRegSettings * CGroupAlignmentsToolManager::x_GetParamsAsRegSetting ( ) protectedvirtual ◆ x_GetParamsAsRegSetting() [7/17] ◆ x_GetParamsAsRegSetting() [8/17] ◆ x_GetParamsAsRegSetting() [9/17] IRegSettings * CMergeAlignmentsToolManager::x_GetParamsAsRegSetting ( ) protectedvirtual ◆ x_GetParamsAsRegSetting() [10/17] ◆ x_GetParamsAsRegSetting() [11/17] ◆ x_GetParamsAsRegSetting() [12/17] ◆ x_GetParamsAsRegSetting() [13/17] ◆ x_GetParamsAsRegSetting() [14/17] IRegSettings * CCommonTaxTreeTool::x_GetParamsAsRegSetting ( ) protectedvirtual ◆ x_GetParamsAsRegSetting() [15/17] IRegSettings * CTreeBuilderTool::x_GetParamsAsRegSetting ( ) protectedvirtual ◆ x_GetParamsAsRegSetting() [16/17] IRegSettings * CAdvancedCleanupTool::x_GetParamsAsRegSetting ( ) protectedvirtual ◆ x_GetParamsAsRegSetting() [17/17] IRegSettings * CCreateNeedlemanWunschToolManager::x_GetParamsAsRegSetting ( ) protectedvirtual ◆ x_GetParamsPanel() [1/19] ◆ x_GetParamsPanel() [2/19] ◆ x_GetParamsPanel() [3/19] ◆ x_GetParamsPanel() [4/19] ◆ x_GetParamsPanel() [5/19] ◆ x_GetParamsPanel() [6/19] ◆ x_GetParamsPanel() [7/19] ◆ x_GetParamsPanel() [8/19] ◆ x_GetParamsPanel() [9/19] ◆ x_GetParamsPanel() [10/19] ◆ x_GetParamsPanel() [11/19] ◆ x_GetParamsPanel() [12/19] ◆ x_GetParamsPanel() [13/19] ◆ x_GetParamsPanel() [14/19] ◆ x_GetParamsPanel() [15/19] ◆ x_GetParamsPanel() [16/19] ◆ x_GetParamsPanel() [17/19] ◆ x_GetParamsPanel() [18/19] ◆ x_GetParamsPanel() [19/19] ◆ x_GetRowSeqLoc() ◆ x_GetSelectedDBItem() ◆ x_GetSeqRangeSelection() ◆ x_GetTool() ◆ x_GetUpdatedGeneCommand() void CCreateGeneModelTask::x_GetUpdatedGeneCommand ( objects::CSeq_entry_Handle  seh, const objects::CSeq_id_Handle &  idh, CCmdComposite *  cmd  ) private

Definition at line 876 of file create_gene_model_tool_manager.cpp.

References CSerialObject::Assign(), SGeneCdsmRnaFeats::cds, cmd, CSeqFeatData_Base::e_Cdregion, CSeqFeatData_Base::e_Gene, CSeqFeatData_Base::e_Rna, CScope::eGetBioseq_All, NStr::EqualCase(), CSeqFeatData::eSubtype_gene, CScope::GetBioseqHandle(), CSeq_feat_Base::GetData(), CSeqFeatData_Base::GetGene(), CSeq_feat_Handle::GetLocationId(), CGene_ref_Base::GetLocus(), GetMappedCDSForProduct(), CSeq_feat_Handle::GetOriginalSeq_feat(), CSeq_entry_Handle::GetScope(), SAnnotSelector::IncludeFeatType(), CSeqFeatData_Base::IsGene(), CScope::IsSameBioseq(), CGene_ref_Base::IsSetLocus(), ITERATE, CCreateGeneModelTask::m_GeneModelMap, CCreateGeneModelTask::m_Scope, NON_CONST_ITERATE, and CCreateGeneModelTask::x_UpdateGeneOnSequence().

Referenced by CCreateGeneModelTask::x_AssignIDsAndUpdateGenes().

◆ x_GetValidInputData() ◆ x_GetWorkingDirectory() [1/2] wxString CMafftToolJob::x_GetWorkingDirectory ( ) const protectedvirtual ◆ x_GetWorkingDirectory() [2/2] virtual wxString CMSAToolJob::x_GetWorkingDirectory ( ) const inlineprotectedvirtual ◆ x_GoFirstPage() bool CNGAlignTool::x_GoFirstPage ( ) protected ◆ x_GoLastPage() bool CNGAlignTool::x_GoLastPage ( ) protected ◆ x_GoNextPage() bool CNGAlignTool::x_GoNextPage ( ) protected ◆ x_GoPrevPage() bool CNGAlignTool::x_GoPrevPage ( ) protected ◆ x_Group_By_GeneID() void CCreateGeneModelTask::x_Group_By_GeneID ( objects::CSeq_annot &  annot, const objects::CSeq_id_Handle &  idh  ) private

Definition at line 672 of file create_gene_model_tool_manager.cpp.

References CSeq_annot_Base::GetData(), CSeq_feat_Base::GetData(), CRange_Base::GetFrom(), CSeq_annot_Base::C_Data::GetFtable(), CSeq_feat_Base::GetLocation(), CRange_Base::GetTo(), CSeq_loc::GetTotalRange(), i, CSeqFeatData_Base::IsGene(), ITERATE, NON_CONST_ITERATE, CCreateGeneModelTask::s_GetGeneID(), CSeq_annot_Base::SetData(), CSeq_feat_Base::SetLocation(), and CCreateGeneModelTask::x_GroupGenes().

Referenced by CCreateGeneModelTask::x_GetCommand().

◆ x_GroupGenes() void CCreateGeneModelTask::x_GroupGenes ( const objects::CSeq_id_Handle &  idh, CRef< objects::CSeq_feat >  gene  ) private ◆ x_HideShowInputs() void CBLASTSearchParamsPanel::x_HideShowInputs ( ) protected

Definition at line 375 of file blast_search_params_panel.cpp.

References CBLASTParams::eSequences, CBLASTParams::GetCurrProgram(), CBLASTParams::GetSubjectType(), CBLASTSearchParamsPanel::ID_STATIC_REPEAT_TYPE, CBLASTParams::IsNucInput(), CBLASTSearchParamsPanel::m_chbStandalone, CBLASTSearchParamsPanel::m_DbGenCodeCombo, CBLASTSearchParamsPanel::m_DbGenCodeLabel, CBLASTSearchParamsPanel::m_LCRegionsCheck, CBLASTSearchParamsPanel::m_Local, CBLASTSearchParamsPanel::m_Params, CBLASTSearchParamsPanel::m_QueryGenCodeCombo, CBLASTSearchParamsPanel::m_QueryGenCodeLabel, CBLASTSearchParamsPanel::m_RepeatsCheck, CBLASTSearchParamsPanel::m_RepeatType, CBLASTSearchParamsPanel::m_ThreshInput, CBLASTSearchParamsPanel::m_ThreshLabel, CBLASTSearchParamsPanel::m_WMDownload, CBLASTSearchParamsPanel::m_WMStaticBoxSizer, CBLASTParams::NeedsDbGeneticCode(), CBLASTParams::NeedsQueryGeneticCode(), CBLASTParams::NeedsThreshold(), and CBLASTSearchParamsPanel::x_UpdateMaskCtrls().

Referenced by CBLASTSearchParamsPanel::TransferDataToWindow().

◆ x_InitGeneticCodesCombo() void CBLASTSearchParamsPanel::x_InitGeneticCodesCombo ( ) protected ◆ x_InitMenuResources() void CAlignSpanView::x_InitMenuResources ( ) protected ◆ x_InitMonitoringStage() void CBlastSearchTask::x_InitMonitoringStage ( TDescriptors &  descriptors ) protected

preapres App Job for monitoring stage of the task

Definition at line 134 of file blast_search_task.cpp.

References CBlastSearchTask::eMonitor, i, CBlastSearchTask::m_CurrTask, CAppTask::m_Descr, CBlastSearchTask::m_LoadingOptions, CBlastSearchTask::m_MonitoringJob, CBlastSearchTask::m_NetBlastDS, CBlastSearchTask::m_SrvLocator, CBlastSearchTask::m_Stage, CBlastSearchTask::m_ToolName, CRef< C, Locker >::Reset(), and CNetBlastMonitoringJob::SetLoadingOptions().

Referenced by CBlastSearchTask::Init_Monitoring(), and CBlastSearchTask::x_NextSubTask().

◆ x_InitProjectParams() [1/3] void CBLASTToolManager::x_InitProjectParams ( ) protected ◆ x_InitProjectParams() [2/3] void CGroupAlignmentsToolManager::x_InitProjectParams ( ) protectedvirtual ◆ x_InitProjectParams() [3/3] void CMergeAlignmentsToolManager::x_InitProjectParams ( ) protectedvirtual ◆ x_InitTaxons() void CBLASTSearchParamsPanel::x_InitTaxons ( ) protected ◆ x_InitWidget() [1/3] void CAlignSpanView::x_InitWidget ( ) protected

Definition at line 222 of file align_span_view.cpp.

References _ASSERT, CAlnMultiDSBuilder::CreateDataSource(), CSeq_align_Base::C_Segs::e_Denseg, CSeq_align_Base::C_Segs::e_Disc, CSeq_align_Base::C_Segs::e_Spliced, CAlnSpanVertModel::fDiscontig, CAlnSpanVertModel::fGap, CAlnSpanVertModel::fIntron, CProjectViewBase::GetScope(), CAlnMultiDSBuilder::Init(), ITERATE, CAlignSpanView::m_AlnWidget, CAlignSpanView::m_DataSource, CAlignSpanView::m_InputAligns, CAlignSpanView::m_Model, CAlignSpanView::m_OrigAlign, CAlignSpanView::m_OrigAnnot, CAlignSpanView::m_OrigBioseq, CRef< C, Locker >::NotNull(), CAlnMultiDSBuilder::PreCreateDataSource(), CwxTableListCtrl::RemoveModel(), CAlnSpanWidget::SetAlnModel(), and CAlnMultiDSBuilder::SetSyncCreate().

Referenced by CAlignSpanView::x_PostAttachToProject().

◆ x_InitWidget() [2/3] void CAnnotCompareView::x_InitWidget ( ) protected ◆ x_InitWidget() [3/3] void CDotMatrixView::x_InitWidget ( ) protected

Definition at line 139 of file dot_matrix_view.cpp.

References _ASSERT, CHitMatrixDSBuilder::CreateDataSource(), CRef< C, Locker >::GetPointer(), CProjectViewBase::GetScope(), GUI_AsyncExec(), CHitMatrixDSBuilder::Init(), CDotMatrixView::m_Aligns, CDotMatrixView::m_AlnWidget, CDotMatrixView::m_DataSource, NULL, CHitMatrixWidget::SetDataSource(), and wxT.

Referenced by CDotMatrixView::x_PostAttachToProject().

◆ x_IsFirstPage() bool CNGAlignTool::x_IsFirstPage ( ) const protected ◆ x_IsLastPage() bool CNGAlignTool::x_IsLastPage ( ) const protected ◆ x_IsNucInput() bool CBLASTToolManager::x_IsNucInput ( ) const protectedvirtual ◆ x_LoadJobDescriptors() void CNetBLASTUIDataSource::x_LoadJobDescriptors ( ) protected

Definition at line 492 of file net_blast_ui_data_source.cpp.

References CNetBLASTUIDataSource::CNetBlastJobDescriptor, CNetBlastJobDescriptor::eInvalidState, Error(), CUser_field_Base::GetData(), CUser_object::GetField(), CException::GetMsg(), CUser_field_Base::C_Data::GetObjects(), i, Info(), kJobDescrPath, kJobsTag, LOG_POST, CNetBLASTUIDataSource::m_JobDescrs, MSerial_AsnText, and CSysPath::ResolvePath().

Referenced by CNetBLASTUIDataSource::Open().

◆ x_LoadPage() bool CNGAlignTool::x_LoadPage ( ) protected ◆ x_LoadSettings() ◆ x_MergeObjects() ◆ x_NeedsConversion() bool CMultiAlignViewFactory::x_NeedsConversion ( const CObject &  object, objects::CScope &  scope  ) private ◆ x_NextSubTask()

prepares the next subtask (makes it current), this function is used for iterating subtasks.

Implements CCompositeAppTask.

Definition at line 202 of file blast_search_task.cpp.

References _ASSERT, CBlastSearchTask::eFinished, CBlastSearchTask::eMonitor, CBlastSearchTask::eRetrieve, CBlastSearchTask::eSubmit, CNetBlastSubmittingJob::GetDescriptors(), CBlastSearchTask::m_CurrTask, CBlastSearchTask::m_MonitoringJob, CBlastSearchTask::m_Stage, CBlastSearchTask::m_SubmittingJob, CRef< C, Locker >::Reset(), and CBlastSearchTask::x_InitMonitoringStage().

◆ x_NotifyDataSource() void CNetBlastJobDescriptor::x_NotifyDataSource ( ) protected ◆ x_OnDatabaseSelected() void CBLAST_DB_Dialog::x_OnDatabaseSelected ( ) protected ◆ x_OnInputTypeChanged() void CBLASTSearchOptionsPanel::x_OnInputTypeChanged ( bool  nuc_input ) protected

Definition at line 545 of file blast_search_options_panel.cpp.

References CBLASTParams::GetCurrProgram(), CBLASTParams::GetProgramLabel(), CBLASTParams::GetProgramLabels(), CBLASTParams::IsNucInput(), CBLASTSearchOptionsPanel::m_Params, CBLASTSearchOptionsPanel::m_ProgramCombo, ToArrayString(), ToWxString(), CBLASTSearchOptionsPanel::x_FillQueryList(), CBLASTSearchOptionsPanel::x_UpdateQuerySeqSet(), and CBLASTSearchOptionsPanel::x_UpdateSubjects().

Referenced by CBLASTSearchOptionsPanel::OnNucRadioSelected(), CBLASTSearchOptionsPanel::OnProtRadioSelected(), and CBLASTSearchOptionsPanel::TransferDataToWindow().

◆ x_OnJobDescrChanged() [1/2] void CNetBLAST_DMSearchForm::x_OnJobDescrChanged ( CEvent *  ) protected ◆ x_OnJobDescrChanged() [2/2] ◆ x_OnSetSelection() [1/7] ◆ x_OnSetSelection() [2/7]

override in derived classes in order to handle selection broadcast

override this function in derived classes

Reimplemented from CProjectView.

Definition at line 252 of file annot_compare_view.cpp.

◆ x_OnSetSelection() [3/7]

override in derived classes in order to handle selection broadcast

override this function in derived classes

Reimplemented from CProjectView.

Definition at line 255 of file cross_align_view.cpp.

References CRangeCollection< Position >::clear(), CSelectionEvent::GetAllObjects(), CSelectionEvent::GetRangeSelection(), CSelectionEvent::GetScope(), IHit::GetSeqAlign(), CSelectionEvent::HasObjectSelection(), CSelectionEvent::HasRangeSelection(), ITERATE, CCrossAlignView::m_AlnWidget, CCrossAlignView::m_DataSource, CSelectionEvent::Match(), CCrossAlnWidget::SetObjectSelection(), CCrossAlnWidget::SetQueryRangeSelection(), CCrossAlnWidget::SetSubjectRangeSelection(), CRangeCollection< Position >::size(), and CProjectViewBase::x_GetScope().

◆ x_OnSetSelection() [4/7]

override in derived classes in order to handle selection broadcast

override this function in derived classes

Reimplemented from CProjectView.

Definition at line 259 of file dot_matrix_view.cpp.

References _ASSERT, CRangeCollection< Position >::clear(), CSelectionEvent::GetAllObjects(), CSelectionEvent::GetRangeSelection(), CSelectionEvent::GetScope(), IHit::GetSeqAlign(), CSelectionEvent::HasObjectSelection(), CSelectionEvent::HasRangeSelection(), ITERATE, CDotMatrixView::m_AlnWidget, CDotMatrixView::m_DataSource, CSelectionEvent::Match(), CHitMatrixWidget::SetObjectSelection(), CHitMatrixWidget::SetQueryRangeSelection(), CHitMatrixWidget::SetSubjectRangeSelection(), CRangeCollection< Position >::size(), and CProjectViewBase::x_GetScope().

◆ x_OnSetSelection() [5/7]

override in derived classes in order to handle selection broadcast

override this function in derived classes

Reimplemented from CProjectView.

Definition at line 363 of file mp_cross_align_view.cpp.

◆ x_OnSetSelection() [6/7]

override in derived classes in order to handle selection broadcast

override this function in derived classes

Reimplemented from CProjectView.

Definition at line 418 of file multi_align_view.cpp.

References _ASSERT, CRef< C, Locker >::Empty(), CSelectionEvent::GetIdLocs(), CSelectionEvent::GetIds(), CObjectIndex::GetMatches(), CSelRowHandle::GetNumrow(), CSelectionEvent::GetRangeSelection(), CSelectionEvent::GetRangeSelectionAsLocs(), CSelectionEvent::GetScope(), CSelectionEvent::HasObjectSelection(), CSelectionEvent::HasRangeSelection(), ITERATE, CMultiAlignView::m_AlnWidget, CMultiAlignView::m_DataSource, CMultiAlignView::m_ObjIndex, match(), NULL, results, row, CAlnMultiWidget::Select(), CAlnMultiWidget::SetSelection(), CSelectionEvent::sm_MatchAlnLocs, and CProjectViewBase::x_GetScope().

◆ x_OnSetSelection() [7/7]

override in derived classes in order to handle selection broadcast

override this function in derived classes

Reimplemented from CProjectView.

Definition at line 1264 of file phy_tree_view.cpp.

References CPhyloTree::ClearSelection(), copy(), CBioTreeSelection::GetBioTree(), CPhyloTreeDataSource::GetDictionary(), CBioTreeSelection::GetExplicitlySelectedNodeIds(), CPhyloTree::GetFeatureDict(), CBioTreeSelection::GetFeatureId(), CBioTreeSelection::GetFeatureValue(), CBioTreeFeatureDictionary::GetId(), CSelectionEvent::GetIdLocs(), CSelectionEvent::GetIds(), CSelectionEvent::GetIndexed(), CObjectIndex::GetMatches(), CBioTreeSelection::GetNodeIds(), CSelNodeHandle::GetNodeIdx(), visitor_taxid_query::GetNodes(), visitor_string_query::GetNodes(), CConstRef< C, Locker >::GetNonNullPointer(), CRef< C, Locker >::GetPointer(), CSelectionEvent::GetScope(), CSelectionEvent::GetTaxIDs(), CPhyloTreeDataSource::GetTree(), CPhyTreeView::GetWidget(), CBioTreeSelection::HasFeature(), CBioTreeFeatureDictionary::HasFeature(), CSelectionEvent::HasObjectSelection(), set< Key, Compare >::insert(), ITERATE, CPhyTreeView::m_BioTreeContainer, CPhyTreeView::m_DataSource, CPhyTreeView::m_ObjectIndex, NULL, CPhyloTreeWidget::OnUpdateSelChanged(), results, CPhyloTree::SetExplicitlySelected(), CPhyloTree::SetLeavesExplicitlySelected(), CPhyloTree::SetSelection(), CPhyloTree::SetSelectionIDs(), CSelectionEvent::sm_TreeBroadcastOneToOne, CSelectionEvent::sm_TreeBroadcastProperties, TreeDepthFirst(), and CProjectViewBase::x_HasProject().

◆ x_OnSubjInputTypeChanged() void CBLASTSearchOptionsPanel::x_OnSubjInputTypeChanged ( ) protected ◆ x_PostAttachToProject() [1/4] void CAlignSpanView::x_PostAttachToProject ( ) protectedvirtual ◆ x_PostAttachToProject() [2/4] void CAnnotCompareView::x_PostAttachToProject ( ) protectedvirtual ◆ x_PostAttachToProject() [3/4] void CCrossAlignView::x_PostAttachToProject ( ) protectedvirtual

Reimplemented from CProjectView.

Definition at line 164 of file cross_align_view.cpp.

References _ASSERT, CHitMatrixDSBuilder::CreateDataSource(), CRef< C, Locker >::GetPointer(), CProjectViewBase::GetScope(), CHitMatrixDSBuilder::Init(), CCrossAlignView::m_AlnWidget, CCrossAlignView::m_DataSource, CCrossAlignView::m_OrigAlign, CCrossAlignView::m_OrigAnnot, NULL, CCrossAlnWidget::SetDataSource(), CProjectViewBase::x_HasProject(), and CProjectViewBase::x_UpdateContentLabel().

◆ x_PostAttachToProject() [4/4] void CDotMatrixView::x_PostAttachToProject ( ) protectedvirtual ◆ x_PreAttachToProject() [1/4] ◆ x_PreAttachToProject() [2/4] ◆ x_PreAttachToProject() [3/4] ◆ x_PreAttachToProject() [4/4] ◆ x_QueryStatusChange() void CPhyTreeView::x_QueryStatusChange ( CEvent *  evt ) protected ◆ x_RebuildObjectIndex() void CMultiAlignView::x_RebuildObjectIndex ( ) protectedvirtual ◆ x_RemoveDuplicates() void CCreateGeneModelToolManager::x_RemoveDuplicates ( ) protected ◆ x_ReportErrors() void CBlastSearchTask::x_ReportErrors ( vector< string > &  errors ) protected ◆ x_ResetState() [1/2] void CNetBlastSubmittingJob::x_ResetState ( ) protected ◆ x_ResetState() [2/2] void CNetBlastMonitoringJob::x_ResetState ( ) protected ◆ x_Run() [1/3] void CNetBlastSubmittingJob::x_Run ( void  ) protected

this fucntions performs real work

Definition at line 130 of file blast_jobs.cpp.

References _ASSERT, CLabel::eDefault, CLabel::GetLabel(), CException::GetMsg(), i, Info(), LOG_POST, CNetBlastSubmittingJob::m_Descriptors, CNetBlastSubmittingJob::m_Mutex, CNetBlastSubmittingJob::m_SeqLocs, SeqLocToBioseq(), CSeq_entry_Base::SetSeq(), CBioseq_set_Base::SetSeq_set(), str(), string, CException::what(), and CNetBlastSubmittingJob::x_AddError().

Referenced by CNetBlastSubmittingJob::Run().

◆ x_Run() [2/3]

this functions performs real work every call to this function does pools each job once, then functions exits if some of jobs are still pending it returns eRunning state, so that it can be executed one more time

Definition at line 335 of file blast_jobs.cpp.

References CNetBLASTUIDataSource::DeleteJobDescriptors(), done, IAppJob::eCanceled, CNetBlastJobDescriptor::eCompleted, IAppJob::eCompleted, CNetBlastJobDescriptor::eExpired, CNetBlastJobDescriptor::eFailed, CNetBlastJobDescriptor::eRetrieved, IAppJob::eRunning, i, CJobCancelable::IsCanceled(), CNetBlastMonitoringJob::m_Descriptors, CNetBlastMonitoringJob::m_Errors, CNetBlastMonitoringJob::m_Mutex, CNetBlastMonitoringJob::m_NetBlastDS, t, and CNetBlastMonitoringJob::x_StartRetrivingTask().

Referenced by CNetBlastMonitoringJob::Run().

◆ x_Run() [3/3]

override this function in derived classes

Reimplemented from CAppTask.

Definition at line 280 of file create_gene_model_tool_manager.cpp.

References _ASSERT, CSelectProjectOptions::AddItemsToWorkspace(), cmd, data, IAppTask::eCanceled, IAppTask::eCompleted, IAppTask::eFailed, ICommandProccessor::Execute(), CGBDocument::GetUndoManager(), CCreateGeneModelTask::m_Items, SCreateGeneModelParams::m_MergeResults, CCreateGeneModelTask::m_Options, CCreateGeneModelTask::m_Params, CCreateGeneModelTask::m_Scope, CCreateGeneModelTask::m_Service, CPrefetchSeqDescr::PrefetchSeqDescr(), and CCreateGeneModelTask::x_GetCommand().

◆ x_RunCurrentSubTask() ◆ x_SaveJobDescriptors() void CNetBLASTUIDataSource::x_SaveJobDescriptors ( ) protected

Definition at line 454 of file net_blast_ui_data_source.cpp.

References CUser_object::AddField(), Error(), CException::GetMsg(), i, Info(), CNetBlastJobDescriptor::IsDeleted(), kJobDescrPath, kJobsTag, LOG_POST, CNetBLASTUIDataSource::m_JobDescrs, MSerial_AsnText, CSysPath::ResolvePath(), CUser_object_Base::SetType(), and CNetBlastJobDescriptor::ToUserObject().

Referenced by CNetBLASTUIDataSource::Close().

◆ x_SaveSettings() ◆ x_SelectCompatibleInputObjects() [1/18] void CBLASTToolManager::x_SelectCompatibleInputObjects ( ) protectedvirtual

Definition at line 416 of file blast_tool_manager.cpp.

References AsyncConvertObjects(), map_checker< Container >::begin(), map_checker< Container >::clear(), set< Key, Compare >::clear(), convert(), map_checker< Container >::end(), map_checker< Container >::erase(), CSeq_entry_CI::fIncludeGivenEntry, map_checker< Container >::find(), CSeq_entry_CI::fRecursive, CSeq_loc::GetId(), CBioseq_Handle::GetSeqId(), i, map_checker< Container >::insert(), set< Key, Compare >::insert(), CBioseq_Handle::IsNa(), kSelectedSequences, CBLASTToolManager::m_InputObjects, CBLASTToolManager::m_NucObjects, CBLASTToolManager::m_ProtObjects, and CSeq_loc::SetWhole().

Referenced by CBLASTToolManager::QuickLaunch(), and CBLASTToolManager::x_CreateOptionsPanelIfNeeded().

◆ x_SelectCompatibleInputObjects() [2/18] void CCleanupAlignmentsToolManager::x_SelectCompatibleInputObjects ( ) protected ◆ x_SelectCompatibleInputObjects() [3/18] void CClustalOmegaTool::x_SelectCompatibleInputObjects ( ) protected ◆ x_SelectCompatibleInputObjects() [4/18] void CClustalwTool::x_SelectCompatibleInputObjects ( ) protected ◆ x_SelectCompatibleInputObjects() [5/18] void CCreateGeneModelToolManager::x_SelectCompatibleInputObjects ( ) protected ◆ x_SelectCompatibleInputObjects() [6/18] void CFindOverlapTool::x_SelectCompatibleInputObjects ( ) protectedvirtual ◆ x_SelectCompatibleInputObjects() [7/18] void CGroupAlignmentsToolManager::x_SelectCompatibleInputObjects ( ) protected ◆ x_SelectCompatibleInputObjects() [8/18] void CKalignTool::x_SelectCompatibleInputObjects ( ) protectedvirtual ◆ x_SelectCompatibleInputObjects() [9/18] void CMafftTool::x_SelectCompatibleInputObjects ( ) protectedvirtual ◆ x_SelectCompatibleInputObjects() [10/18] void CMergeAlignmentsToolManager::x_SelectCompatibleInputObjects ( ) protected ◆ x_SelectCompatibleInputObjects() [11/18] void CMuscleTool::x_SelectCompatibleInputObjects ( ) protectedvirtual ◆ x_SelectCompatibleInputObjects() [12/18] void CNGAlignTool::x_SelectCompatibleInputObjects ( ) protectedvirtual ◆ x_SelectCompatibleInputObjects() [13/18] void CProSplignTool::x_SelectCompatibleInputObjects ( ) protectedvirtual

Definition at line 198 of file prosplign_tool.cpp.

References map_checker< Container >::clear(), copy(), CSeq_loc::GetId(), CBioseq_Handle::IsAa(), CSeq_loc_Base::IsInt(), CBioseq_Handle::IsNa(), CSeq_loc_Base::IsWhole(), CProSplignTool::m_NAObjects, CProSplignTool::m_ProteinObjects, NON_CONST_ITERATE, results, and CAlgoToolManagerBase::x_ConvertInputObjects().

Referenced by CProSplignTool::x_CreateParamsPanelIfNeeded().

◆ x_SelectCompatibleInputObjects() [14/18] void CSplignTool::x_SelectCompatibleInputObjects ( ) protectedvirtual

Definition at line 122 of file splign_tool.cpp.

References map_checker< Container >::clear(), copy(), CSeqdesc_Base::e_Molinfo, CMolInfo_Base::eBiomol_genomic, CMolInfo_Base::eBiomol_peptide, CMolInfo_Base::eBiomol_unknown, CMolInfo_Base::GetBiomol(), CSeq_loc::GetId(), CSeqdesc_Base::GetMolinfo(), CSeq_loc_Base::IsInt(), CSeq_loc_Base::IsWhole(), CSplignTool::m_GenomicObjects, CSplignTool::m_NAObjects, NON_CONST_ITERATE, results, and CAlgoToolManagerBase::x_ConvertInputObjects().

Referenced by CSplignTool::QuickLaunch(), and CSplignTool::x_CreateParamsPanelIfNeeded().

◆ x_SelectCompatibleInputObjects() [15/18] void CCommonTaxTreeTool::x_SelectCompatibleInputObjects ( ) protected ◆ x_SelectCompatibleInputObjects() [16/18] void CTreeBuilderTool::x_SelectCompatibleInputObjects ( ) protectedvirtual ◆ x_SelectCompatibleInputObjects() [17/18] void CAdvancedCleanupTool::x_SelectCompatibleInputObjects ( ) protectedvirtual ◆ x_SelectCompatibleInputObjects() [18/18] void CCreateNeedlemanWunschToolManager::x_SelectCompatibleInputObjects ( ) protected ◆ x_SetStatusText() [1/2] void CNetBlastSubmittingJob::x_SetStatusText ( const string &  text ) protected ◆ x_SetStatusText() [2/2] void CNetBlastMonitoringJob::x_SetStatusText ( const string &  text ) protected ◆ x_ShowWM() void CBLASTSearchParamsPanel::x_ShowWM ( bool  show ) protected ◆ x_StartRetrivingTask() void CNetBlastMonitoringJob::x_StartRetrivingTask ( const vector< string > &  RIDs ) protected ◆ x_StartTask() ◆ x_StoreGeneratedFeats() void CCreateGeneModelTask::x_StoreGeneratedFeats ( const objects::CSeq_annot &  annot, TGeneCDSmRNAList &  gene_cds_rna  ) const private ◆ x_ToUserObject()

converts SProgParams into CUser_object

Definition at line 625 of file blast_search_params.cpp.

References CUser_object::AddField(), kBLASTParamsTag, kDbGeneticCodeTag, keValueTag, kFilterLowComplexTag, kGeneticCodeTag, kMaskLowercaseTag, kMaskRepeatsTag, kThresholdTag, kWordSizeTag, CBLASTParams::SProgParams::m_DbGeneticCode, CBLASTParams::SProgParams::m_eValue, CBLASTParams::SProgParams::m_FilterLowComplex, CBLASTParams::SProgParams::m_MaskLowercase, CBLASTParams::SProgParams::m_MaskRepeats, CBLASTParams::SProgParams::m_QueryGeneticCode, CBLASTParams::SProgParams::m_Threshold, CBLASTParams::SProgParams::m_WordSize, CBLASTParams::NeedsDbGeneticCode(), CBLASTParams::NeedsQueryGeneticCode(), CBLASTParams::NeedsThreshold(), CRef< C, Locker >::Release(), and CUser_object_Base::SetType().

Referenced by CBLASTParams::ToUserObject().

◆ x_Update() void CAlignSpanView::x_Update ( ) protectedvirtual ◆ x_UpdateCollapsedState() void CBLAST_DB_Dialog::x_UpdateCollapsedState ( wxTreeItemId  id ) protected ◆ x_UpdateDBCombo() void CBLASTSearchOptionsPanel::x_UpdateDBCombo ( ) protected

Definition at line 863 of file blast_search_options_panel.cpp.

References CMRUList< T >::AddItem(), arr, db_map_base< K, T >::end(), db_map_base< K, T >::find(), CBLASTParams::GetCurrDatabase(), CBLASTParams::GetCurrProgram(), CBLASTParams::GetDatabase(), CBLASTDatabases::GetDbMap(), CBLASTDatabases::GetDefaultMRU_DBs(), CBLASTDatabases::GetInstance(), CMRUList< T >::GetItems(), CBLASTParams::GetMRUDatabases(), Info(), CBLASTParams::IsNucDatabase(), ITERATE, CBLASTDatabases::Loaded(), LOG_POST, CBLASTSearchOptionsPanel::m_DatabaseCombo, CBLASTSearchOptionsPanel::m_Params, CMRUList< T >::SetItems(), and ToWxString().

Referenced by CBLASTSearchOptionsPanel::OnBrowseDatabases(), CBLASTSearchOptionsPanel::x_CheckDBLoaded(), and CBLASTSearchOptionsPanel::x_UpdateSubjects().

◆ x_UpdateFilterStatusText() void CBLAST_DB_Dialog::x_UpdateFilterStatusText ( bool  reset, int  n  ) protected ◆ x_UpdateGeneOnSequence()

Definition at line 942 of file create_gene_model_tool_manager.cpp.

References _ASSERT, SGeneCdsmRnaFeats::cds, SGeneCdsmRnaFeats::CrossLinkTriple(), eExtreme_Positional, SGeneCdsmRnaFeats::gene, CSeq_feat_Base::GetLocation(), CSeq_feat::GetNamedDbxref(), CSeq_loc::GetStart(), CSeq_loc::GetStop(), CSeq_loc::GetStrand(), CSeq_loc::IsPartialStart(), CSeq_loc::IsPartialStop(), ITERATE, SGeneCdsmRnaFeats::mRNA, NCBI_USER_THROW, NON_CONST_ITERATE, CRef< C, Locker >::Reset(), CSeq_feat_Base::ResetPartial(), CSeq_feat_Base::SetLocation(), CSeq_feat_Base::SetPartial(), and CCreateGeneModelTask::sGeneDbName.

Referenced by CCreateGeneModelTask::x_GetUpdatedGeneCommand().

◆ x_UpdateMaskCtrls() void CBLASTSearchParamsPanel::x_UpdateMaskCtrls ( ) protected ◆ x_UpdateQuerySeqSet() void CBLASTSearchOptionsPanel::x_UpdateQuerySeqSet ( ) protected

Definition at line 580 of file blast_search_options_panel.cpp.

References i, CBLASTParams::IsNucInput(), kSelectedSequences, CBLASTSearchOptionsPanel::m_CurrentQuerySet, CBLASTSearchOptionsPanel::m_NucObjects, CBLASTSearchOptionsPanel::m_Params, CBLASTSearchOptionsPanel::m_ProtObjects, CBLASTSearchOptionsPanel::m_QuerySeqSetCombo, CBLASTSearchOptionsPanel::m_QuerySeqSetStatic, s_UseSets(), ToStdString(), and ToWxString().

Referenced by CBLASTSearchOptionsPanel::x_OnInputTypeChanged().

◆ x_UpdateStatusMessage() void CAlignSpanView::x_UpdateStatusMessage ( ) protectedvirtual

Definition at line 589 of file align_span_view.cpp.

References CAlnSpanWidget::GetNumRowsSelected(), CwxTableListCtrl::GetNumRowsVisible(), NStr::IntToString(), CAlignSpanView::m_AlnWidget, CAlignSpanView::m_Model, CAlignSpanView::m_StatusBar, and ToWxString().

Referenced by CAlignSpanView::OnProjectChanged(), CAlignSpanView::OnWidgetRangeChanged(), CAlignSpanView::OnWidgetSelChanged(), CAlignSpanView::x_OnSetSelection(), CAlignSpanView::x_PostAttachToProject(), and CAlignSpanView::x_Update().

◆ x_UpdateSubjects() void CBLASTSearchOptionsPanel::x_UpdateSubjects ( ) protected

Definition at line 670 of file blast_search_options_panel.cpp.

References CBLASTParams::eLocalDB, CBLASTParams::eNCBIDB, CBLASTParams::GetLocalNucDB(), CBLASTParams::GetLocalProtDB(), CBLASTParams::GetSubjectType(), CBLASTParams::IsSubjNucInput(), CBLASTSearchOptionsPanel::m_LocalDBCtrl, CBLASTSearchOptionsPanel::m_Params, CBLASTSearchOptionsPanel::x_FillSubjectList(), CBLASTSearchOptionsPanel::x_UpdateDBCombo(), and CBLASTSearchOptionsPanel::x_UpdateSubjectSeqSet().

Referenced by CBLASTSearchOptionsPanel::OnProgramComboSelected(), CBLASTSearchOptionsPanel::x_OnInputTypeChanged(), and CBLASTSearchOptionsPanel::x_UpdateSubjectType().

◆ x_UpdateSubjectSeqSet() void CBLASTSearchOptionsPanel::x_UpdateSubjectSeqSet ( ) protected

Definition at line 687 of file blast_search_options_panel.cpp.

References i, CBLASTParams::IsSubjNucInput(), kSelectedSequences, CBLASTSearchOptionsPanel::m_CurrentSubjectSet, CBLASTSearchOptionsPanel::m_NucObjects, CBLASTSearchOptionsPanel::m_Params, CBLASTSearchOptionsPanel::m_ProtObjects, CBLASTSearchOptionsPanel::m_SubjectSeqSetCombo, CBLASTSearchOptionsPanel::m_SubjectSeqSetStatic, s_UseSets(), ToStdString(), and ToWxString().

Referenced by CBLASTSearchOptionsPanel::x_UpdateSubjects().

◆ x_UpdateSubjectType() void CBLASTSearchOptionsPanel::x_UpdateSubjectType ( ) protected

Definition at line 942 of file blast_search_options_panel.cpp.

References CBLASTDatabases::eInitial, CBLASTParams::eLocalDB, CBLASTParams::eNCBIDB, CBLASTParams::GetSubjectType(), CBLASTSearchOptionsPanel::m_DBLoadState, CBLASTSearchOptionsPanel::m_LocalDBSizer, CBLASTSearchOptionsPanel::m_LocalSeqsSizer, CBLASTSearchOptionsPanel::m_LocalSizer, CBLASTSearchOptionsPanel::m_NCBIDBSizer, CBLASTSearchOptionsPanel::m_Params, CBLASTSearchOptionsPanel::m_SubjectSeqSetCombo, CBLASTSearchOptionsPanel::m_SubjectSeqSetStatic, CBLASTSearchOptionsPanel::x_CheckDBLoaded(), and CBLASTSearchOptionsPanel::x_UpdateSubjects().

Referenced by CBLASTSearchOptionsPanel::OnSubjectLocalDBSelected(), CBLASTSearchOptionsPanel::OnSubjectNCBIDBSelected(), CBLASTSearchOptionsPanel::OnSubjectSequencesSelected(), and CBLASTSearchOptionsPanel::TransferDataToWindow().

◆ x_ValidateParams() [1/18] bool CBLASTToolManager::x_ValidateParams ( ) protected ◆ x_ValidateParams() [2/18] bool CCleanupAlignmentsToolManager::x_ValidateParams ( ) protectedvirtual ◆ x_ValidateParams() [3/18] bool CClustalOmegaTool::x_ValidateParams ( ) protectedvirtual

validates user input in Parameters panel, report errors if any

validate parameters after Params page override this function in derived classes

Reimplemented from CAlgoToolManagerBase.

Definition at line 98 of file clustal_omega_tool.cpp.

◆ x_ValidateParams() [4/18] bool CClustalwTool::x_ValidateParams ( ) protectedvirtual

validates user input in Parameters panel, report errors if any

validate parameters after Params page override this function in derived classes

Reimplemented from CAlgoToolManagerBase.

Definition at line 98 of file clustalw_tool.cpp.

◆ x_ValidateParams() [5/18] bool CCreateGeneModelToolManager::x_ValidateParams ( ) protectedvirtual ◆ x_ValidateParams() [6/18] bool CFindOverlapTool::x_ValidateParams ( ) protectedvirtual

validates user input in Parameters panel, report errors if any

validate parameters after Params page override this function in derived classes

Reimplemented from CAlgoToolManagerBase.

Definition at line 124 of file find_overlap_tool.cpp.

◆ x_ValidateParams() [7/18] bool CGroupAlignmentsToolManager::x_ValidateParams ( ) protectedvirtual ◆ x_ValidateParams() [8/18] bool CKalignTool::x_ValidateParams ( ) protectedvirtual

validates user input in Parameters panel, report errors if any

validate parameters after Params page override this function in derived classes

Reimplemented from CAlgoToolManagerBase.

Definition at line 97 of file kalign_tool.cpp.

◆ x_ValidateParams() [9/18] bool CMafftTool::x_ValidateParams ( ) protectedvirtual

validates user input in Parameters panel, report errors if any

validate parameters after Params page override this function in derived classes

Reimplemented from CAlgoToolManagerBase.

Definition at line 97 of file mafft_tool.cpp.

◆ x_ValidateParams() [10/18] bool CMergeAlignmentsToolManager::x_ValidateParams ( ) protectedvirtual ◆ x_ValidateParams() [11/18] bool CMuscleTool::x_ValidateParams ( ) protectedvirtual

validates user input in Parameters panel, report errors if any

validate parameters after Params page override this function in derived classes

Reimplemented from CAlgoToolManagerBase.

Definition at line 97 of file muscle_tool.cpp.

◆ x_ValidateParams() [12/18] bool CNetBLAST_DMSearchJob::x_ValidateParams ( ) protectedvirtual ◆ x_ValidateParams() [13/18] bool CNGAlignTool::x_ValidateParams ( ) protectedvirtual

validates user input in Parameters panel, report errors if any

validate parameters after Params page override this function in derived classes

Reimplemented from CAlgoToolManagerBase.

Definition at line 259 of file ngalign_tool.cpp.

◆ x_ValidateParams() [14/18] bool CProSplignTool::x_ValidateParams ( ) protectedvirtual

validates user input in Parameters panel, report errors if any

validate parameters after Params page override this function in derived classes

Reimplemented from CAlgoToolManagerBase.

Definition at line 164 of file prosplign_tool.cpp.

◆ x_ValidateParams() [15/18] bool CSplignTool::x_ValidateParams ( ) protectedvirtual

validates user input in Parameters panel, report errors if any

validate parameters after Params page override this function in derived classes

Reimplemented from CAlgoToolManagerBase.

Definition at line 117 of file splign_tool.cpp.

◆ x_ValidateParams() [16/18] bool CCommonTaxTreeTool::x_ValidateParams ( ) protectedvirtual

validates user input in Parameters panel, report errors if any

validate parameters after Params page override this function in derived classes

Reimplemented from CAlgoToolManagerBase.

Definition at line 98 of file taxtree_tool.cpp.

◆ x_ValidateParams() [17/18] bool CTreeBuilderTool::x_ValidateParams ( ) protectedvirtual

validates user input in Parameters panel, report errors if any

validate parameters after Params page override this function in derived classes

Reimplemented from CAlgoToolManagerBase.

Definition at line 139 of file tree_builder_tool.cpp.

◆ x_ValidateParams() [18/18] bool CAdvancedCleanupTool::x_ValidateParams ( ) protectedvirtual

validates user input in Parameters panel, report errors if any

validate parameters after Params page override this function in derived classes

Reimplemented from CAlgoToolManagerBase.

Definition at line 93 of file advanced_cleanup_tool.cpp.

◆ ~CBLAST_DB_Dialog() ◆ ~CBLAST_Dlg_Item() CBLAST_Dlg_Item::~CBLAST_Dlg_Item ( ) ◆ ~CBLASTSearchOptionsPanel() ◆ ~CBLASTSearchParamsPanel() ◆ ~CBlastSearchTask() ◆ ~CCleanupAlignmentsParamsPanel() ◆ ~CClustalOmegaToolParams() ◆ ~CClustalwToolParams() ◆ ~CCreateGeneModelTask() ◆ ~CFindOverlapPanel() ◆ ~CFindOverlapParams() ◆ ~CGroupAlignmentsParamsPanel() ◆ ~CKalignToolParams() ◆ ~CMafftToolParams() ◆ ~CMergeAlignmentsParamsPanel() ◆ ~CMSAToolJob() CMSAToolJob::~CMSAToolJob ( ) virtual ◆ ~CMuscleToolPanel() ◆ ~CMuscleToolParams() ◆ ~CNeedlemanWunschToolParams() ◆ ~CNetBLAST_DMSearchForm() CNetBLAST_DMSearchForm::~CNetBLAST_DMSearchForm ( ) virtual ◆ ~CNetBlastDMSearchFormPanel() ◆ ~CNetBlastJobDescriptor() ◆ ~CNetBLASTLoadOptionPanel() ◆ ~CNetBLASTUIDataSource() CNetBLASTUIDataSource::~CNetBLASTUIDataSource ( ) virtual ◆ ~CNGAlignPanel() ◆ ~CNGAlignParams() ◆ ~CPhyTreeView() CPhyTreeView::~CPhyTreeView ( ) ◆ ~CSplignPanel() ◆ ~CSplignParams() ◆ ~CTaxTreeToolPanel() ◆ ~CTaxTreeToolParams() ◆ ~CTreeBuilderPanel() ◆ ~CTreeBuilderParams() ◆ ~SGeneCdsmRnaFeats() ◆ cds CRef<objects::CSeq_feat> SGeneCdsmRnaFeats::cds ◆ gene CRef<objects::CSeq_feat> SGeneCdsmRnaFeats::gene ◆ m_AdvancedParams string CBLASTParams::m_AdvancedParams protected ◆ m_AdvParams [1/2] wxString CBLASTSearchParamsPanel::m_AdvParams protected ◆ m_AdvParams [2/2] wxString CNGAlignParams::m_AdvParams private ◆ m_Algo ◆ m_AlgoSelector wxComboBox* CCleanupAlignmentsParamsPanel::m_AlgoSelector ◆ m_Alignments [1/8] ◆ m_Alignments [2/8] ◆ m_Alignments [3/8] ◆ m_Alignments [4/8] ◆ m_Alignments [5/8] ◆ m_Alignments [6/8] ◆ m_Alignments [7/8] ◆ m_Alignments [8/8] ◆ m_Aligns [1/2] ◆ m_Aligns [2/2] ◆ m_AlnMgr_FillUnaligned [1/2] bool SCleanupAlignmentsParams::m_AlnMgr_FillUnaligned ◆ m_AlnMgr_FillUnaligned [2/2] wxCheckBox* CCleanupAlignmentsParamsPanel::m_AlnMgr_FillUnaligned ◆ m_AlnMgr_PreserveRows [1/2] bool SCleanupAlignmentsParams::m_AlnMgr_PreserveRows ◆ m_AlnMgr_PreserveRows [2/2] wxCheckBox* CCleanupAlignmentsParamsPanel::m_AlnMgr_PreserveRows ◆ m_AlnMgr_Sort [1/2] bool SCleanupAlignmentsParams::m_AlnMgr_Sort ◆ m_AlnMgr_Sort [2/2] wxCheckBox* CCleanupAlignmentsParamsPanel::m_AlnMgr_Sort ◆ m_AlnMgr_Transloc [1/2] bool SCleanupAlignmentsParams::m_AlnMgr_Transloc ◆ m_AlnMgr_Transloc [2/2] wxCheckBox* CCleanupAlignmentsParamsPanel::m_AlnMgr_Transloc ◆ m_AlnWidget [1/4] ◆ m_AlnWidget [2/4] ◆ m_AlnWidget [3/4] ◆ m_AlnWidget [4/4]

Definition at line 150 of file multi_align_view.hpp.

Referenced by CMultiAlignView::CreateViewWindow(), CMultiAlignView::DestroyViewWindow(), CMultiAlignView::GetSelection(), CMultiAlignView::GetWindow(), CMultiAlignView::LoadSettings(), CMultiAlignView::OnDSChanged(), CMultiAlignView::OnProjectChanged(), CMultiAlignView::SaveSettings(), CMultiAlignView::SetRegistryPath(), CMultiAlignView::x_GetSeqRangeSelection(), and CMultiAlignView::x_OnSetSelection().

◆ m_AnchoredAln ◆ m_AnnWidget ◆ m_AssumeNegStrand wxCheckBox* CMergeAlignmentsParamsPanel::m_AssumeNegStrand ◆ m_AutoDelete ◆ m_AutoFlag bool CMafftToolParams::m_AutoFlag private ◆ m_BandSize int CNeedlemanWunschToolParams::m_BandSize private ◆ m_BestHit bool CNGAlignParams::m_BestHit ◆ m_BioTreeContainer CConstRef<objects::CBioTreeContainer> CPhyTreeView::m_BioTreeContainer private ◆ m_BLASTPanel ◆ m_BlastParams wxString CFindOverlapParams::m_BlastParams private ◆ m_BlockEvents bool CNetBlastDMSearchFormPanel::m_BlockEvents protected ◆ m_BrowseDBBtn wxBitmapButton* CBLASTSearchOptionsPanel::m_BrowseDBBtn ◆ m_Btc CRef<objects::CBioTreeContainer> CPhyloTreeJob::m_Btc private ◆ m_Builder ◆ m_CatItems ◆ m_cDNA_strand int CSplignParams::m_cDNA_strand private ◆ m_cDNAList ◆ m_CDNAListAccValidator ◆ m_cDNASeqs ◆ m_chbStandalone wxCheckBox* CBLASTSearchParamsPanel::m_chbStandalone ◆ m_ChildItems ◆ m_ClustalOmegaPath wxString CClustalOmegaToolParams::m_ClustalOmegaPath private ◆ m_ClustalWPath wxString CClustalwToolParams::m_ClustalWPath private ◆ m_CmdLine wxString CMSAToolJob::m_CmdLine protected ◆ m_Command ◆ m_CommandLine [1/5] wxString CClustalOmegaToolParams::m_CommandLine private ◆ m_CommandLine [2/5] wxString CClustalwToolParams::m_CommandLine private ◆ m_CommandLine [3/5] wxString CKalignToolParams::m_CommandLine private ◆ m_CommandLine [4/5] wxString CMafftToolParams::m_CommandLine private ◆ m_CommandLine [5/5] wxString CMuscleToolParams::m_CommandLine private ◆ m_CompartCheck wxCheckBox* CBLASTSearchParamsPanel::m_CompartCheck ◆ m_Completed bool CNetBlastDMSearchFormPanel::m_Completed protected ◆ m_CompPenalty double CSplignParams::m_CompPenalty private ◆ m_ConstructMethod wxString CTreeBuilderParams::m_ConstructMethod private ◆ m_Cont CRef<objects::CBioTreeContainer> CPhyTreeView::m_Cont mutableprivate ◆ m_CurrentMethod ◆ m_CurrentNode ◆ m_CurrentPage int CNGAlignTool::m_CurrentPage protected ◆ m_CurrentQuerySet string CBLASTSearchOptionsPanel::m_CurrentQuerySet protected ◆ m_CurrentSubjectSet string CBLASTSearchOptionsPanel::m_CurrentSubjectSet protected ◆ m_CurrTask ◆ m_data [1/5] ◆ m_data [2/5] ◆ m_data [3/5] ◆ m_data [4/5] ◆ m_data [5/5] ◆ m_DatabaseCombo wxComboBox* CBLASTSearchOptionsPanel::m_DatabaseCombo ◆ m_DataSource [1/8] ◆ m_DataSource [2/8] ◆ m_DataSource [3/8] ◆ m_DataSource [4/8] ◆ m_DataSource [5/8] ◆ m_DataSource [6/8] ◆ m_DataSource [7/8] ◆ m_DataSource [8/8] ◆ m_DbGenCodeCombo wxComboBox* CBLASTSearchParamsPanel::m_DbGenCodeCombo ◆ m_DbGenCodeLabel wxStaticText* CBLASTSearchParamsPanel::m_DbGenCodeLabel ◆ m_DbGeneticCode [1/2] int CBLASTParams::SProgParams::m_DbGeneticCode ◆ m_DbGeneticCode [2/2] wxString CBLASTSearchParamsPanel::m_DbGeneticCode protected ◆ m_DbItems ◆ m_DBLoadState int CBLASTSearchOptionsPanel::m_DBLoadState protected ◆ m_DbMap ◆ m_DBSizer wxBoxSizer* CBLASTSearchOptionsPanel::m_DBSizer ◆ m_Deleted bool CNetBlastJobDescriptor::m_Deleted protected ◆ m_Descr [1/6] string CNetBlastSubmittingJob::m_Descr protected ◆ m_Descr [2/6] string CNetBlastMonitoringJob::m_Descr protected ◆ m_Descr [3/6] ◆ m_Descr [4/6] ◆ m_Descr [5/6] ◆ m_Descr [6/6] ◆ m_Description string CNetBlastJobDescriptor::m_Description protected ◆ m_Descriptor [1/2] ◆ m_Descriptor [2/2] CUIObject CNetBLASTUILoadManager::m_Descriptor protected ◆ m_Descriptors [1/3] ◆ m_Descriptors [2/3] ◆ m_Descriptors [3/3] ◆ m_Direction int SMergeAlignmentsParams::m_Direction ◆ m_DiscType int CSplignParams::m_DiscType private ◆ m_DistanceMethod wxString CTreeBuilderParams::m_DistanceMethod private ◆ m_Done float CCreateNeedlemanWunschJob::m_Done protected ◆ m_EditUpdate bool CPhyTreeView::m_EditUpdate private ◆ m_EndGapDetect bool CSplignParams::m_EndGapDetect private ◆ m_EntrezQuery string CBLASTParams::m_EntrezQuery protected ◆ m_Error [1/2] ◆ m_Error [2/2] ◆ m_Errors [1/4] vector<string> CNetBlastSubmittingJob::m_Errors protected ◆ m_Errors [2/4] vector<string> CNetBlastMonitoringJob::m_Errors protected ◆ m_Errors [3/4] vector<string> CNetBlastLoadingJob::m_Errors protected ◆ m_Errors [4/4] string CNetBlastJobDescriptor::m_Errors protected ◆ m_eValue [1/3] double CBLASTParams::SProgParams::m_eValue ◆ m_eValue [2/3] double CBLASTSearchParamsPanel::m_eValue protected ◆ m_eValue [3/3] double CNGAlignParams::m_eValue private ◆ m_Expanded bool CBLAST_Dlg_Item::m_Expanded protected ◆ m_Expired bool CNetBlastDMSearchFormPanel::m_Expired protected ◆ m_Failed bool CNetBlastDMSearchFormPanel::m_Failed protected ◆ m_FileNames [1/3] vector<wxString> CTextAlignObjectLoader::m_FileNames private ◆ m_FileNames [2/3] vector<wxString> CPslLoadManager::m_FileNames protected ◆ m_FileNames [3/3] vector<wxString> CTextAlignLoaderManager::m_FileNames protected ◆ m_FillUnaligned [1/2] bool SMergeAlignmentsParams::m_FillUnaligned ◆ m_FillUnaligned [2/2] wxCheckBox* CMergeAlignmentsParamsPanel::m_FillUnaligned ◆ m_FilterLowComplex [1/2] bool CBLASTParams::SProgParams::m_FilterLowComplex ◆ m_FilterLowComplex [2/2] bool CBLASTSearchParamsPanel::m_FilterLowComplex protected ◆ m_FilterMode int CNGAlignParams::m_FilterMode private ◆ m_FilterQty int CFindOverlapParams::m_FilterQty private ◆ m_FilterStr string CNetBLAST_DMSearchQuery::m_FilterStr ◆ m_FirstSeqFreeEnds int CNeedlemanWunschToolParams::m_FirstSeqFreeEnds private ◆ m_GapExtendCost int CNeedlemanWunschToolParams::m_GapExtendCost private ◆ m_GapOpenCost int CNeedlemanWunschToolParams::m_GapOpenCost private ◆ m_GeneModelMap ◆ m_GeneralSizer wxFlexGridSizer* CBLASTSearchParamsPanel::m_GeneralSizer ◆ m_GenerateTree [1/3] bool CClustalOmegaToolParams::m_GenerateTree private ◆ m_GenerateTree [2/3] bool CClustalwToolParams::m_GenerateTree private ◆ m_GenerateTree [3/3] bool CMuscleToolParams::m_GenerateTree private ◆ m_GenomicList ◆ m_GenomicListAccValidator ◆ m_GenomicObjects ◆ m_GenomicSeq ◆ m_GroupByEST [1/2] bool SGroupAlignmentsParams::m_GroupByEST ◆ m_GroupByEST [2/2] wxCheckBox* CGroupAlignmentsParamsPanel::m_GroupByEST ◆ m_GroupByGenBank [1/2] bool SGroupAlignmentsParams::m_GroupByGenBank ◆ m_GroupByGenBank [2/2] wxCheckBox* CGroupAlignmentsParamsPanel::m_GroupByGenBank ◆ m_GroupByHTGS [1/2] bool SGroupAlignmentsParams::m_GroupByHTGS ◆ m_GroupByHTGS [2/2] wxCheckBox* CGroupAlignmentsParamsPanel::m_GroupByHTGS ◆ m_GroupByLikeTaxId [1/2] bool SGroupAlignmentsParams::m_GroupByLikeTaxId ◆ m_GroupByLikeTaxId [2/2] wxCheckBox* CGroupAlignmentsParamsPanel::m_GroupByLikeTaxId ◆ m_GroupByPatent [1/2] bool SGroupAlignmentsParams::m_GroupByPatent ◆ m_GroupByPatent [2/2] wxCheckBox* CGroupAlignmentsParamsPanel::m_GroupByPatent ◆ m_GroupByPredictedRefSeq [1/2] bool SGroupAlignmentsParams::m_GroupByPredictedRefSeq ◆ m_GroupByPredictedRefSeq [2/2] wxCheckBox* CGroupAlignmentsParamsPanel::m_GroupByPredictedRefSeq ◆ m_GroupByRefSeq [1/2] bool SGroupAlignmentsParams::m_GroupByRefSeq ◆ m_GroupByRefSeq [2/2] wxCheckBox* CGroupAlignmentsParamsPanel::m_GroupByRefSeq ◆ m_GroupBySeqId [1/2] bool SGroupAlignmentsParams::m_GroupBySeqId ◆ m_GroupBySeqId [2/2] wxCheckBox* CGroupAlignmentsParamsPanel::m_GroupBySeqId ◆ m_GroupByStrand [1/2] bool SGroupAlignmentsParams::m_GroupByStrand ◆ m_GroupByStrand [2/2] wxCheckBox* CGroupAlignmentsParamsPanel::m_GroupByStrand ◆ m_GroupByTaxId [1/2] bool SGroupAlignmentsParams::m_GroupByTaxId ◆ m_GroupByTaxId [2/2] wxCheckBox* CGroupAlignmentsParamsPanel::m_GroupByTaxId ◆ m_GroupByWGS [1/2] bool SGroupAlignmentsParams::m_GroupByWGS ◆ m_GroupByWGS [2/2] wxCheckBox* CGroupAlignmentsParamsPanel::m_GroupByWGS ◆ m_HitFilter_MinIdentity [1/2] float SCleanupAlignmentsParams::m_HitFilter_MinIdentity ◆ m_HitFilter_MinIdentity [2/2] wxTextCtrl* CCleanupAlignmentsParamsPanel::m_HitFilter_MinIdentity ◆ m_HitFilter_MinLength [1/2] int SCleanupAlignmentsParams::m_HitFilter_MinLength ◆ m_HitFilter_MinLength [2/2] wxTextCtrl* CCleanupAlignmentsParamsPanel::m_HitFilter_MinLength ◆ m_Id wxTreeItemId CBLAST_Dlg_Item::m_Id protected ◆ m_IdMap ◆ m_InitialLayout int CPhyTreeView::m_InitialLayout private ◆ m_InitialRotateLabels int CPhyTreeView::m_InitialRotateLabels private ◆ m_InitialUseDistances int CPhyTreeView::m_InitialUseDistances private ◆ m_InputAligns ◆ m_InputListDirty [1/3] bool CCleanupAlignmentsParamsPanel::m_InputListDirty private ◆ m_InputListDirty [2/3] bool CGroupAlignmentsParamsPanel::m_InputListDirty protected ◆ m_InputListDirty [3/3] bool CMergeAlignmentsParamsPanel::m_InputListDirty protected ◆ m_InputObjects [1/8] ◆ m_InputObjects [2/8] ◆ m_InputObjects [3/8] ◆ m_InputObjects [4/8] ◆ m_InputObjects [5/8] ◆ m_InputObjects [6/8] ◆ m_InputObjects [7/8] ◆ m_InputObjects [8/8] ◆ m_IsDatabase bool CBLAST_Dlg_Item::m_IsDatabase protected ◆ m_Items ◆ m_JobDescrMutex ◆ m_JobDescrs ◆ m_JobTitle [1/4] string CBLASTParams::m_JobTitle protected ◆ m_JobTitle [2/4] wxString CBLASTSearchParamsPanel::m_JobTitle protected ◆ m_JobTitle [3/4] string CNetBlastJobDescriptor::m_JobTitle protected ◆ m_JobTitle [4/4] wxString CNGAlignParams::m_JobTitle private ◆ m_KalignPath wxString CKalignToolParams::m_KalignPath private ◆ m_Label ◆ m_LabelLength size_t CBLAST_Dlg_Item::m_LabelLength protected ◆ m_LabelPos size_t CBLAST_Dlg_Item::m_LabelPos protected ◆ m_LCRegionsCheck wxCheckBox* CBLASTSearchParamsPanel::m_LCRegionsCheck ◆ m_LeafLabels wxString CTreeBuilderParams::m_LeafLabels private ◆ m_LoadingJob ◆ m_LoadingOptions [1/2] ◆ m_LoadingOptions [2/2] ◆ m_Local bool CBLASTSearchParamsPanel::m_Local protected ◆ m_LocalDBCtrl wxTextCtrl* CBLASTSearchOptionsPanel::m_LocalDBCtrl ◆ m_LocalDBLoader bool CBLASTParams::m_LocalDBLoader protected ◆ m_LocalDBLoaderCtrl wxCheckBox* CBLASTSearchOptionsPanel::m_LocalDBLoaderCtrl ◆ m_LocalDBSizer wxBoxSizer* CBLASTSearchOptionsPanel::m_LocalDBSizer ◆ m_LocalNucDB string CBLASTParams::m_LocalNucDB protected ◆ m_LocalProtDB string CBLASTParams::m_LocalProtDB protected ◆ m_LocalSeqsSizer wxBoxSizer* CBLASTSearchOptionsPanel::m_LocalSeqsSizer ◆ m_LocalSizer wxStaticBoxSizer* CBLASTSearchOptionsPanel::m_LocalSizer ◆ m_LocalWinMaskDirPath string CBLASTToolManager::m_LocalWinMaskDirPath protected ◆ m_LocationSel ◆ m_MafftPath wxString CMafftToolParams::m_MafftPath private ◆ m_MainSplitter wxSplitterWindow* CMPCrossAlignView::m_MainSplitter private ◆ m_Manager [1/2] ◆ m_Manager [2/2] ◆ m_MaskLCRegions bool CBLASTSearchParamsPanel::m_MaskLCRegions protected ◆ m_MaskLowercase bool CBLASTParams::SProgParams::m_MaskLowercase ◆ m_MaskRepeats [1/2] bool CBLASTParams::SProgParams::m_MaskRepeats ◆ m_MaskRepeats [2/2] bool CBLASTSearchParamsPanel::m_MaskRepeats protected ◆ m_MatchCost int CNeedlemanWunschToolParams::m_MatchCost private ◆ m_MaxGenomicExtent long CSplignParams::m_MaxGenomicExtent private ◆ m_MaxIntron long CSplignParams::m_MaxIntron private ◆ m_MaxSlop wxString CFindOverlapParams::m_MaxSlop private ◆ m_MergeAlgo int SMergeAlignmentsParams::m_MergeAlgo ◆ m_MergeFlags int SMergeAlignmentsParams::m_MergeFlags ◆ m_MergeQuerySeqOnly wxCheckBox* CMergeAlignmentsParamsPanel::m_MergeQuerySeqOnly ◆ m_MinCompIdentity double CSplignParams::m_MinCompIdentity private ◆ m_MinExonIdentity double CSplignParams::m_MinExonIdentity private ◆ m_MismatchCost int CNeedlemanWunschToolParams::m_MismatchCost private ◆ m_Model ◆ m_MolType ◆ m_MonitoringJob ◆ m_MRUQueries ◆ m_MusclePath wxString CMuscleToolParams::m_MusclePath private ◆ m_Mutex [1/3] ◆ m_Mutex [2/3] ◆ m_Mutex [3/3] CMutex CNetBlastJobDescriptor::m_Mutex mutableprotected

Definition at line 118 of file net_blast_job_descr.hpp.

Referenced by CNetBlastJobDescriptor::Check(), CNetBlastJobDescriptor::GetDescription(), CNetBlastJobDescriptor::GetErrors(), CNetBlastJobDescriptor::GetJobTitle(), CNetBlastJobDescriptor::GetRemoteBlast(), CNetBlastJobDescriptor::GetRID(), CNetBlastJobDescriptor::GetSubmitTime(), CNetBlastJobDescriptor::Init(), CNetBlastJobDescriptor::MarkDeleted(), CNetBlastJobDescriptor::Release(), CNetBlastJobDescriptor::Retrieve(), and CNetBlastJobDescriptor::Submit().

◆ m_NAObjects [1/2] ◆ m_NAObjects [2/2] ◆ m_NCBIDBSizer wxFlexGridSizer* CBLASTSearchOptionsPanel::m_NCBIDBSizer ◆ m_NeedsDbGenCode ◆ m_NeedsQueryGenCode ◆ m_NeedsThreshold ◆ m_NetBlastDS [1/5] ◆ m_NetBlastDS [2/5] ◆ m_NetBlastDS [3/5] ◆ m_NetBlastDS [4/5] ◆ m_NetBlastDS [5/5] ◆ m_NucDatabase string CBLASTParams::m_NucDatabase protected ◆ m_NucDB ◆ m_NucInput [1/2] ◆ m_NucInput [2/2] bool CBLASTParams::m_NucInput protected ◆ m_NucMRUDatabases ◆ m_NucObjects [1/2] ◆ m_NucObjects [2/2] ◆ m_NucProgram ◆ m_NucRadio wxRadioButton* CBLASTSearchOptionsPanel::m_NucRadio ◆ m_Numrow ◆ m_Object ◆ m_ObjectIndex ◆ m_ObjectList [1/2] ◆ m_ObjectList [2/2] ◆ m_ObjectListCtrl ◆ m_Objects [1/15] ◆ m_Objects [2/15] ◆ m_Objects [3/15] ◆ m_Objects [4/15] ◆ m_Objects [5/15] ◆ m_Objects [6/15] ◆ m_Objects [7/15] ◆ m_Objects [8/15] ◆ m_Objects [9/15] ◆ m_Objects [10/15] ◆ m_Objects [11/15] ◆ m_Objects [12/15] ◆ m_Objects [13/15] ◆ m_Objects [14/15] TObjects CTextAlignObjectLoader::m_Objects private ◆ m_Objects [15/15] ◆ m_ObjIndex ◆ m_OKBtn wxButton* CBLAST_DB_Dialog::m_OKBtn ◆ m_Open bool CNetBLASTUIDataSource::m_Open protected ◆ m_OptionPanel ◆ m_Options ◆ m_OptionsPage [1/2] ◆ m_OptionsPage [2/2] CPage CTextAlignLoaderManager::m_OptionsPage protected ◆ m_OptionsPanel ◆ m_OrigAlign [1/4] ◆ m_OrigAlign [2/4] ◆ m_OrigAlign [3/4] ◆ m_OrigAlign [4/4] CConstRef<objects::CSeq_align> CMultiAlignView::m_OrigAlign protected ◆ m_OrigAnnot [1/4] ◆ m_OrigAnnot [2/4] ◆ m_OrigAnnot [3/4] ◆ m_OrigAnnot [4/4] CConstRef<objects::CSeq_annot> CMultiAlignView::m_OrigAnnot protected ◆ m_OrigBioseq ◆ m_Panel [1/16] wxPanel* CAlignSpanView::m_Panel private ◆ m_Panel [2/16] ◆ m_Panel [3/16] ◆ m_Panel [4/16] ◆ m_Panel [5/16] ◆ m_Panel [6/16] ◆ m_Panel [7/16] ◆ m_Panel [8/16] ◆ m_Panel [9/16] ◆ m_Panel [10/16] wxPanel* CPhyTreeView::m_Panel private ◆ m_Panel [11/16] ◆ m_Panel [12/16] ◆ m_Panel [13/16] ◆ m_Panel [14/16] ◆ m_Panel [15/16] ◆ m_Panel [16/16] ◆ m_Params [1/40]

Definition at line 234 of file blast_search_options_panel.hpp.

Referenced by CBLASTSearchOptionsPanel::Init(), CBLASTSearchOptionsPanel::OnBrowseDatabases(), CBLASTSearchOptionsPanel::OnDatabaseComboSelected(), CBLASTSearchOptionsPanel::OnLocalDBLoaderClick(), CBLASTSearchOptionsPanel::OnProgramComboSelected(), CBLASTSearchOptionsPanel::OnSelectLocalDB(), CBLASTSearchOptionsPanel::OnSubjectLocalDBSelected(), CBLASTSearchOptionsPanel::OnSubjectNCBIDBSelected(), CBLASTSearchOptionsPanel::OnSubjectSequencesSelected(), CBLASTSearchOptionsPanel::RestoreDefaults(), CBLASTSearchOptionsPanel::SetParams(), CBLASTSearchOptionsPanel::TransferDataFromWindow(), CBLASTSearchOptionsPanel::TransferDataToWindow(), CBLASTSearchOptionsPanel::x_CheckDBLoaded(), CBLASTSearchOptionsPanel::x_FillQueryList(), CBLASTSearchOptionsPanel::x_FillSubjectList(), CBLASTSearchOptionsPanel::x_OnInputTypeChanged(), CBLASTSearchOptionsPanel::x_UpdateDBCombo(), CBLASTSearchOptionsPanel::x_UpdateQuerySeqSet(), CBLASTSearchOptionsPanel::x_UpdateSubjects(), CBLASTSearchOptionsPanel::x_UpdateSubjectSeqSet(), and CBLASTSearchOptionsPanel::x_UpdateSubjectType().

◆ m_Params [2/40] ◆ m_Params [3/40] ◆ m_Params [4/40] ◆ m_Params [5/40] ◆ m_Params [6/40] ◆ m_Params [7/40] ◆ m_Params [8/40] ◆ m_Params [9/40] ◆ m_Params [10/40] ◆ m_Params [11/40] ◆ m_Params [12/40] ◆ m_Params [13/40] ◆ m_Params [14/40] ◆ m_Params [15/40] ◆ m_Params [16/40] ◆ m_Params [17/40] ◆ m_Params [18/40] ◆ m_Params [19/40] ◆ m_Params [20/40] ◆ m_Params [21/40] ◆ m_Params [22/40] ◆ m_Params [23/40] ◆ m_Params [24/40] ◆ m_Params [25/40] ◆ m_Params [26/40] ◆ m_Params [27/40] ◆ m_Params [28/40] ◆ m_Params [29/40] ◆ m_Params [30/40] ◆ m_Params [31/40] ◆ m_Params [32/40] ◆ m_Params [33/40] ◆ m_Params [34/40] ◆ m_Params [35/40] ◆ m_Params [36/40] ◆ m_Params [37/40] ◆ m_Params [38/40] ◆ m_Params [39/40] ◆ m_Params [40/40] ◆ m_ParamsPanel [1/8] ◆ m_ParamsPanel [2/8] wxBoxSizer* CCleanupAlignmentsParamsPanel::m_ParamsPanel ◆ m_ParamsPanel [3/8] ◆ m_ParamsPanel [4/8] ◆ m_ParamsPanel [5/8] ◆ m_ParamsPanel [6/8] ◆ m_ParamsPanel [7/8] ◆ m_ParamsPanel [8/8] ◆ m_Parent ◆ m_ParentWindow [1/4] wxWindow* CBLASTToolManager::m_ParentWindow protected ◆ m_ParentWindow [2/4] wxWindow* CNetBLASTUILoadManager::m_ParentWindow protected ◆ m_ParentWindow [3/4] wxWindow* CPslLoadManager::m_ParentWindow protected ◆ m_ParentWindow [4/4] wxWindow* CTextAlignLoaderManager::m_ParentWindow protected ◆ m_Path string CBLAST_Dlg_Item::m_Path protected ◆ m_pConstruct wxChoice* CTreeBuilderPanel::m_pConstruct ◆ m_pDistance wxChoice* CTreeBuilderPanel::m_pDistance ◆ m_PId ◆ m_pLabels wxChoice* CTreeBuilderPanel::m_pLabels ◆ m_PolyADetect bool CSplignParams::m_PolyADetect private ◆ m_ProcHandle ◆ m_Program ◆ m_ProgramCombo wxComboBox* CBLASTSearchOptionsPanel::m_ProgramCombo ◆ m_ProgToParams ◆ m_ProjectFolderName ◆ m_ProjectParams [1/2] ◆ m_ProjectParams [2/2] ◆ m_ProjectSelPanel ◆ m_ProtDatabase string CBLASTParams::m_ProtDatabase protected ◆ m_ProteinObjects TObjects CProSplignTool::m_ProteinObjects protected ◆ m_ProtMRUDatabases ◆ m_ProtObjects [1/2] ◆ m_ProtObjects [2/2] ◆ m_ProtProgram ◆ m_ProtRadio wxRadioButton* CBLASTSearchOptionsPanel::m_ProtRadio ◆ m_Queries [1/2] ◆ m_Queries [2/2] ◆ m_Query ◆ m_QueryCombo wxComboBox* CBLASTSearchOptionsPanel::m_QueryCombo ◆ m_QueryGenCodeCombo wxComboBox* CBLASTSearchParamsPanel::m_QueryGenCodeCombo ◆ m_QueryGenCodeLabel wxStaticText* CBLASTSearchParamsPanel::m_QueryGenCodeLabel ◆ m_QueryGeneticCode [1/2] int CBLASTParams::SProgParams::m_QueryGeneticCode ◆ m_QueryGeneticCode [2/2] wxString CBLASTSearchParamsPanel::m_QueryGeneticCode protected ◆ m_QueryListCtrl [1/2] ◆ m_QueryListCtrl [2/2] ◆ m_QuerySeqSetCombo wxChoice* CBLASTSearchOptionsPanel::m_QuerySeqSetCombo ◆ m_QuerySeqSetStatic wxStaticText* CBLASTSearchOptionsPanel::m_QuerySeqSetStatic ◆ m_QuietFlag [1/2] bool CKalignToolParams::m_QuietFlag private ◆ m_QuietFlag [2/2] bool CMafftToolParams::m_QuietFlag private ◆ m_Ranges objects::CMappingRanges CMSAToolJob::m_Ranges protected ◆ m_RegPath [1/25] string CAlignSpanView::m_RegPath private ◆ m_RegPath [2/25] string CBLASTToolManager::m_RegPath protected ◆ m_RegPath [3/25] ◆ m_RegPath [4/25] string CCleanupAlignmentsParamsPanel::m_RegPath private ◆ m_RegPath [5/25] string CClustalOmegaToolParams::m_RegPath private ◆ m_RegPath [6/25] string CClustalwToolParams::m_RegPath private ◆ m_RegPath [7/25] string CFindOverlapParams::m_RegPath private ◆ m_RegPath [8/25] string SGroupAlignmentsParams::m_RegPath ◆ m_RegPath [9/25] string CGroupAlignmentsParamsPanel::m_RegPath protected ◆ m_RegPath [10/25] string CKalignToolParams::m_RegPath private ◆ m_RegPath [11/25] string CMafftToolParams::m_RegPath private ◆ m_RegPath [12/25] string SMergeAlignmentsParams::m_RegPath ◆ m_RegPath [13/25] string CMergeAlignmentsParamsPanel::m_RegPath protected ◆ m_RegPath [14/25] string CMultiAlignView::m_RegPath private ◆ m_RegPath [15/25] string CMuscleToolParams::m_RegPath private ◆ m_RegPath [16/25] string CNeedlemanWunschToolParams::m_RegPath private ◆ m_RegPath [17/25] string CNetBLASTUIDataSource::m_RegPath protected ◆ m_RegPath [18/25] string CNetBLASTUILoadManager::m_RegPath protected ◆ m_RegPath [19/25] string CNGAlignParams::m_RegPath private ◆ m_RegPath [20/25] string CSplignPanel::m_RegPath private ◆ m_RegPath [21/25] string CSplignParams::m_RegPath private ◆ m_RegPath [22/25] string CTaxTreeToolParams::m_RegPath ◆ m_RegPath [23/25] string CTreeBuilderParams::m_RegPath private ◆ m_RegPath [24/25] string CPslLoadManager::m_RegPath protected ◆ m_RegPath [25/25] string CTextAlignLoaderManager::m_RegPath protected ◆ m_RemoteBlast CRef<blast::CRemoteBlast> CNetBlastJobDescriptor::m_RemoteBlast protected ◆ m_RepeatLib string CBLASTParams::SProgParams::m_RepeatLib ◆ m_RepeatsCheck wxCheckBox* CBLASTSearchParamsPanel::m_RepeatsCheck ◆ m_RepeatType wxChoice* CBLASTSearchParamsPanel::m_RepeatType ◆ m_ResetBtn wxButton* CNetBlastDMSearchFormPanel::m_ResetBtn ◆ m_Retrieved bool CNetBlastDMSearchFormPanel::m_Retrieved protected ◆ m_RID string CNetBlastJobDescriptor::m_RID protected ◆ m_Root ◆ m_SavedInput string CNetBLASTUILoadManager::m_SavedInput mutableprotected ◆ m_Scheme ◆ m_Scope [1/4] ◆ m_Scope [2/4] CScope* CNetBlastLoadingJob::m_Scope protected ◆ m_Scope [3/4] CRef<objects::CScope> CCreateGeneModelTask::m_Scope private ◆ m_Scope [4/4] CRef<objects::CScope> CTextAlignObjectLoader::m_Scope private ◆ m_ScoringMethod int CMuscleToolParams::m_ScoringMethod private ◆ m_ScoringMethods ◆ m_SearchCtrl [1/2] wxTextCtrl* CBLAST_DB_Dialog::m_SearchCtrl ◆ m_SearchCtrl [2/2] wxTextCtrl* CNetBlastDMSearchFormPanel::m_SearchCtrl ◆ m_SearchValue wxString CNetBlastDMSearchFormPanel::m_SearchValue protected ◆ m_SecondSeqFreeEnds int CNeedlemanWunschToolParams::m_SecondSeqFreeEnds private ◆ m_SelDatabase string CBLAST_DB_Dialog::m_SelDatabase protected ◆ m_Seq1 ◆ m_Seq1List [1/2] ◆ m_Seq1List [2/2] ◆ m_Seq2 ◆ m_Seq2List ◆ m_Seq_id ◆ m_SeqIds [1/4] ◆ m_SeqIds [2/4] ◆ m_SeqIds [3/4] ◆ m_SeqIds [4/4] ◆ m_SeqLocs [1/3] ◆ m_SeqLocs [2/3] ◆ m_SeqLocs [3/3] ◆ m_SeqTypes ◆ m_Service ◆ m_SortInput wxCheckBox* CMergeAlignmentsParamsPanel::m_SortInput ◆ m_Sparse bool CMultiAlignView::m_Sparse protected ◆ m_SrvLocator [1/8] ◆ m_SrvLocator [2/8] ◆ m_SrvLocator [3/8] ◆ m_SrvLocator [4/8] ◆ m_SrvLocator [5/8] ◆ m_SrvLocator [6/8] ◆ m_SrvLocator [7/8] ◆ m_SrvLocator [8/8] ◆ m_Stage ◆ m_State [1/5] EState CBLASTToolManager::m_State protected ◆ m_State [2/5] EState CNetBlastJobDescriptor::m_State protected ◆ m_State [3/5] EState CNetBLASTUILoadManager::m_State protected ◆ m_State [4/5] EState CPslLoadManager::m_State protected ◆ m_State [5/5] EState CTextAlignLoaderManager::m_State protected ◆ m_States TStates CNetBLAST_DMSearchQuery::m_States ◆ m_Status [1/2] string CNetBlastSubmittingJob::m_Status protected ◆ m_Status [2/2] string CNetBlastMonitoringJob::m_Status protected ◆ m_StatusBar wxStatusBar* CAlignSpanView::m_StatusBar private ◆ m_StatusText wxStaticText* CBLAST_DB_Dialog::m_StatusText ◆ m_StyleCatalog ◆ m_Subject [1/2] ◆ m_Subject [2/2] ◆ m_SubjectListCtrl [1/2] ◆ m_SubjectListCtrl [2/2] ◆ m_SubjectSeqSetCombo wxChoice* CBLASTSearchOptionsPanel::m_SubjectSeqSetCombo ◆ m_SubjectSeqSetStatic wxStaticText* CBLASTSearchOptionsPanel::m_SubjectSeqSetStatic ◆ m_SubjectType ◆ m_SubjectTypeLDBCtrl wxRadioButton* CBLASTSearchOptionsPanel::m_SubjectTypeLDBCtrl ◆ m_SubjectTypeNCBICtrl wxRadioButton* CBLASTSearchOptionsPanel::m_SubjectTypeNCBICtrl ◆ m_SubjectTypeSeqsCtrl wxRadioButton* CBLASTSearchOptionsPanel::m_SubjectTypeSeqsCtrl ◆ m_SubjSeqLocs ◆ m_Submitted bool CNetBlastDMSearchFormPanel::m_Submitted protected ◆ m_SubmitTime time_t CNetBlastJobDescriptor::m_SubmitTime protected ◆ m_SubmittingJob ◆ m_TargetProject ◆ m_ThreshInput wxTextCtrl* CBLASTSearchParamsPanel::m_ThreshInput ◆ m_ThreshLabel wxStaticText* CBLASTSearchParamsPanel::m_ThreshLabel ◆ m_Threshold [1/2] int CBLASTParams::SProgParams::m_Threshold ◆ m_Threshold [2/2] long CBLASTSearchParamsPanel::m_Threshold protected ◆ m_Timer wxTimer CBLASTSearchOptionsPanel::m_Timer protected ◆ m_TmpIn wxString CMSAToolJob::m_TmpIn protected ◆ m_TmpOut wxString CMSAToolJob::m_TmpOut protected ◆ m_TmpTreeOut wxString CMSAToolJob::m_TmpTreeOut protected ◆ m_Tool ◆ m_ToolName [1/4] string CNetBlastMonitoringJob::m_ToolName protected ◆ m_ToolName [2/4] string CBLASTSearchOptionsPanel::m_ToolName protected ◆ m_ToolName [3/4] string CBlastSearchTask::m_ToolName protected ◆ m_ToolName [4/4] wxString CMSAToolJob::m_ToolName protected ◆ m_TreeCtrl wxTreeCtrl* CBLAST_DB_Dialog::m_TreeCtrl ◆ m_TruncateOverlap wxCheckBox* CMergeAlignmentsParamsPanel::m_TruncateOverlap ◆ m_Type ◆ m_TypeDescr [1/3] ◆ m_TypeDescr [2/3] ◆ m_TypeDescr [3/3] ◆ m_UseDustFilter ◆ m_UseNucForMixInput bool CBLASTToolManager::m_UseNucForMixInput mutableprotected ◆ m_ViewManager [1/2] ◆ m_ViewManager [2/2] ◆ m_Views TViews CMPCrossAlignView::m_Views private ◆ m_Visible bool CBLAST_Dlg_Item::m_Visible protected ◆ m_WaitPeriodIndex int CNetBlastMonitoringJob::m_WaitPeriodIndex protected ◆ m_WM_Dir [1/2] ◆ m_WM_Dir [2/2] string CNGAlignParams::m_WM_Dir private ◆ m_WM_TaxId [1/2] int CBLASTParams::SProgParams::m_WM_TaxId ◆ m_WM_TaxId [2/2] int CNGAlignParams::m_WM_TaxId private ◆ m_WMDownload wxButton* CBLASTSearchParamsPanel::m_WMDownload ◆ m_WMStatic wxStaticText* CBLASTSearchParamsPanel::m_WMStatic ◆ m_WMStaticBoxSizer wxStaticBoxSizer* CBLASTSearchParamsPanel::m_WMStaticBoxSizer ◆ m_WMTaxIds wxChoice* CBLASTSearchParamsPanel::m_WMTaxIds ◆ m_WordSize [1/3] int CBLASTParams::SProgParams::m_WordSize ◆ m_WordSize [2/3] long CBLASTSearchParamsPanel::m_WordSize protected ◆ m_WordSize [3/3] long CNGAlignParams::m_WordSize private ◆ mf_FindComparts ◆ mf_Standalone ◆ mRNA CRef<objects::CSeq_feat> SGeneCdsmRnaFeats::mRNA ◆ sGeneDbName ◆ sm_ProgramToAttr ◆ CAlignNeedlemanWunschPanel ◆ CAlignSpanViewFactory ◆ CAnnotCompareViewFactory ◆ CClustalOmegaToolPanel ◆ CClustalwToolPanel ◆ CCrossAlignViewFactory ◆ CDotMatrixViewFactory ◆ CFindOverlapPanel ◆ CKalignToolPanel ◆ CMafftToolPanel ◆ CMPCrossAlignViewFactory ◆ CMultiAlignViewFactory ◆ CMuscleToolPanel ◆ CNetBlastDSEvtHandler ◆ CNetBlastJobDescriptor ◆ CNetBLASTUIDataSource ◆ CNGAlignBLASTPanel ◆ CNGAlignPanel ◆ CPhyTreeViewFactory ◆ CSplignPanel ◆ CTaxTreeToolPanel ◆ CTreeBuilderPanel ◆ CTreeBuilderTool

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